I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE 

# Peer Review Meeting of EPA’s Draft Report: Connectivity of Streams and Wetlands to Downstream Waters – A Review and Synthesis

of the Scientific Evidence

Post-Meeting Comments

February 16, 2012i I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE



# Contents

Introduction ........................................

................................................... ..............................1
Reviewers’ Highlights from Meeting Discussions ........

................................................... ....3
Post-Meeting Responses to Charge Questions .............

................................................... ....5 Introductory Comments

.................................................. ................................................... ................. 7

1. This report concludes that all streams, regardless of f low duration or size, are physically, chemically, and biologically connected to rivers; and these connections, individually or cumulatively, exert a strong influence on the character and functioning of downstream waters. ...... 12
a) Are these conclusions supported by the scientific evidence? .

................................................... .. 12
b) Does the report include the most relevant peer-reviewed l iterature on these topics, including evidence of connectivity and isolation? If not please indicate which references are mi ssing. ...... 17
c) Was the reviewed literature cited and summarized corr ectly? If not please indicate where correction or revision is needed. .....................

................................................... ........................ 24

2. This report concludes that open water and wetlands in r iparian areas and floodplains of streams and rivers are physically, chemically, and biologically connec ted with the river network, and that their functions exert a strong influence on the char acter and functioning of downstream waters. ...........................................

................................................... ............................................. 27
a) Are these conclusions supported by the scientific evidence? .

................................................... .. 27
b) Does the report include the most relevant peer-reviewed l iterature on these topics, including evidence of connectivity and isolation? If not please indicate which references are mi ssing. ...... 30
c) Was the reviewed literature cited and summarized corr ectly? If not please indicate where correction or revision is needed. .....................

................................................... ........................ 32

3. This report concludes that for non-riparian/non-floodplain wet lands that are not connected to the river network through a stream channel (i.e., geographica lly isolated wetlands and wetlands that spill into losing streams), connectivity and isolation vary within a watershed and over time, making it difficult to generalize about their connections t o, or isolation from, downstream waters. The literature we reviewed does not provide suffici ent information to evaluate the degree of connectivity (absolute or relative) of these non-ripari an particular wetlands. ................... 34
a) Are these conclusions supported by the scientific evidence? .

................................................... .. 34
b) Does the report include the most relevant peer-reviewed l iterature on these topics, including evidence of connectivity and isolation? If not please indicate which references are mi ssing. ...... 43
c) Was the reviewed literature cited and summarized corr ectly? If not please indicate where correction or revision is needed. .....................

................................................... ........................ 44ii I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE 4. This report concludes that while the influence of a parti cular stream or wetland on downstream waters might be small, the aggregate contribution by an en tire class of streams or wetlands (e.g., all ephemeral streams in the river network, or a cluster of small wetlands) might be substantial. ..... 46
a) Is this conclusion supported by the scientific evidence? ......

................................................... .... 46
b) Does the report include the most relevant peer-reviewed l iterature on this topic? If not please indicate which references are missing. ..............

................................................... ...................... 48
c) Was the reviewed literature cited and summarized corr ectly? If not please indicate where correction or revision is needed. .....................

................................................... ........................ 49


### Additional Reviewer Comments ..........................

................................................... .......... 51
David J. Cooper, Ph.D. ............................

................................................... .......................................... 53 William G. Crumpton, Ph.D. ..........................

................................................... ................................... 55 Kenneth W. Cummings, Ph.D. ............................

................................................... .............................. 57 Walter K. Dodds, Ph.D. .............................

................................................... ........................................ 63 James W. La Baugh, Ph.D. ...........................

................................................... ..................................... 65 Mark C. Rains, Ph.D. ..............................

................................................... .......................................... 71 John S. Richardson, Ph.D. ............................

................................................... ..................................... 81 Joel W. Snodgrass, Ph.D. .............................

................................................... ..................................... 83 Arnold van der Valk, Ph.D. ...........................

................................................... .................................... 87 Mark S. Wipfli, Ph.D. ..............................

................................................... ......................................... 89 

### Appendix A: Individual Reviewer Comments .............. ................................................. A -1
David J. Cooper, Ph.D. ............................

................................................... ........................................ A-3 William G. Crumpton, Ph.D. ..........................

................................................... ............................... A-11 Kenneth W. Cummins, Ph.D. ............................

................................................... ............................ A-21 Walter K. Dodds, Ph.D. .............................

................................................... .................................... A-37 James W. La Baugh, Ph.D. ...........................

................................................... ................................. A-45 Mark C. Rains, Ph.D. ..............................

................................................... ...................................... A-59 John S. Richardson, Ph.D. ............................

................................................... ................................. A-79 Joel W. Snodgrass, Ph.D. .............................

................................................... ................................. A-87 Arnold van der Valk, Ph.D. ...........................

................................................... ................................ A-99 Mark S. Wipfli, Ph.D. ..............................

................................................... ................................... A-107 William R. Wise, Ph.D (Pre-meeting comments only). .....

................................................... ........... A-115 

### Appendix B: Meeting Agenda ..........................

................................................... ............ B-1
Appendix C: List of Reviewers........................

................................................... ............ C-1 Appendix D: List of Observers........................

................................................... ............ D-11 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE



## Introduction

The U.S. Environmental Protection Agency’s (EPA’s) Nationa l Center for Environmental Assessment (NCEA) developed a draft report entitled “ Connectivity of Streams and Wetlands to Downstream Waters: A Review and Synthesis of the Scientific Evidence,” for which Eastern Research Group, Inc. (ERG) organized an independent peer review under Task Order 121, contract EP-C- 07-024. The purpose of the review was to identify any problems, errors, or necessary improvements to the report prior to being published or otherwise released as a final document. ERG was responsible for ide ntifying and selecting the expert reviewers, managing the review, organizing and facilitating a one-day peer review meeting, and preparing the peer review summary report.

ERG identified and secured the services of eleven national ly recognized experts (Appendix C) to conduct this review:

• David J. Cooper, Ph.D., Colorado State University

• William G. Crumpton, Ph.D., Iowa State University

• Kenneth W. Cummins, Ph.D., Humbolt State University

• Walter K. Dodds, Ph.D., Kansas State University

• James W. La Baugh, Ph.D., U.S. Geological Survey

• Mark C. Rains, Ph.D., University of South Florida

• John S. Richardson, Ph.D., University of British Columbia

• Joel W. Snodgrass, Ph.D., Towson University

• Arnold van der Valk, Ph.D., Iowa State University

• Mark S. Wipfli, Ph.D., U.S. Geological Survey

• William R. Wise, Ph.D., University of Florida 1

ERG provided the reviewers with a letter of instruction and the technical charge, which asked for their comments on the various aspects of the draft report. In the first stage of the review, the experts worked individually to prepare written pre-meeting comments, which were provided to all reviewers and EPA prior to a one-day peer review meeting. In the second stage, ERG c onvened the one-day meeting on January 31, 2012, at a venue in Washington, DC (Appendix B provides a copy of the agenda). Ten of the eleven reviewers participated in the workshop; Dr. Wise was not able to at tend.
The meeting was closed to the public and considered an inte rnal EPA deliberative process. Observers from EPA and the U.S. Army Corps of Engineers attended to liste n to the discussions. The list of observers is provided in Appendix D. The meeting process was facilitated by Ms. Kate Schalk, of ERG, and the technical discussions were led by Dr. Walter Dodd. At the close of t he meeting, the reviewers developed some brief highlights of their discussions, which follow this introduction . After the meeting, reviewers revised their premeeting comments to reflect their views as they had evolved based on the meeting discussions. The reviewers’ final post-meeting comments are provided in thi s report. These comments reflect the individual opinions of the reviewers.

1 Since Dr. Wise was unable to attend the workshop, onl y his pre-meeting comments are included.3 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE 

## Reviewers’ Highlights from Meeting Discussions

Peer Review Meeting for EPA Draft Report: Connectivity of Streams and Wetlands to Downstream Waters - A Re view

and Synthesis of the Scientific Evidence

The reviewers’ highlights were prepared by the peer reviewers in the closing session of the peer review meeting held on January 31, 2012. Dr. Walter Dodds, the technica l chair, led the discussions. Post-meeting, peer reviewers reviewed the highlights produced onsite and provided any clarifications or edits, which were considered and incorporated into paragraph below.
We applaud the authors for a document that has integrated a diverse literature and in principle we agree with the overall conclusions of the report. Chemical, physical and biological connectivity are common features of streams and wetlands. This connection can have clear influ ence on downstream waters. The case for the influence is strongest for streams (headwaters including ephemeral and intermittent) and for wetlands on flood plains. The evidence for the influence is not as st rong for some wetland types but many are strongly connected to downstream waters. The introduction needs an ove rarching spatial and temporal conceptual model of the gradients of connectivity across landscapes, a nd the physical and ecological processes that support connectivity. The introductory framework of source, sink , refuge, lag, and transformation should be followed throughout the document. The document should be reviewe d for consistent and accurate terminology and should employ a more appropriate classification scheme for wetlands. The aggregate downstream influences of streams and wetlands should be c onsidered in the introduction and the individual chapters (or in its own chapter), and such consideration sh ould help guide the synthesis. The last section of the report should provide a truly synthetic statement about the connectivity and downstream effects of nonnavigable waters.5 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE 

## Post-Meeting Responses to Charge QuestionsResponses to Charge Questions

7 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE 

### Introductory Comments (Not all reviewers provided introductory comments.)

Reviewer Comments
Cooper The authors of the report have done an excellent job of bringi ng together a huge and

scattered literature. The report was difficult to r ead due to its length, and I find it hard to imagine that most people will use this anything other than a reference document. The literature review indicates that our knowledge of hydrologic connec tions between tributary streams and wetlands and waters of the U.S. is conceptual, with case studies in several portions of the U.S. but large regions, such as western mo untains, and southwestern deserts, where little is known. A few things should be clari fied to make this report more useful. The report focuses on what we know. I would suggest that eac h section of the report must have a discussion of what is unknown or uncertainties about c onnections, functions, and what future research is needed to support our understand of thes e processes. The report gives the impression that we know most of what is needed to u nderstand and regulate these tributaries and wetlands. I think this is only partially correct. The temporal aspect of these jurisdictional identificati ons should be clarified. For example jurisdictional wetlands, under S404, must have flooding or soil sat uration for a certain number of days during the growing season. One day of satur ation is insufficient, but 14 days is typically sufficient. However this report does no t clarify how many hours, days, or weeks per year a tributary must flow into a water of the U. S. to be considered jurisdictional. For an ephemeral stream in Arizona that is tributary to a water of the U.S. is it sufficient if this stream flows on average 1 or 2 days per year, and in some years never flows? For a non-continuous wetland how often does the surface or subsurface connection have to occur? How often do the cited ecological functions, i.e., sediment retention, have to occur? These concepts are critical to have a definitive and objective jurisdictional approach. After the panel meeting I’m still unsure how to i nclude every single channel across the U.S. into a single framework of ecological functioning.
Methods for measuring ecological function should be reviewed and included in this report. The U.S. has spent millions of dollars supporting the Adam us methods, Wetland Evaluation Technique, HGM and other approaches that all h ave been extensively peer reviewed and used in the U.S. I include a few key refere nces at the end of my comments. Methods such as these are critical for inclusion because a ny field activities would need a framework for how to evaluate function or nexus between any stream or wetland and a downstream water.
I understand the importance of identifying “similarly situa ted waters” as a way of extending our understanding beyond single sites. However, the geomorp hic context of such sites must be carefully evaluated. This is no simple mat ter and no method for doing such comparisons is presented in the report.
The definitions used in this report need significant improvem ent. For example wetlands, riparian, floodplain, non-riparian wetland, etc. are all i n need of greater clarification. I suggest not using the Cowardin et al. (1979) definition of wetland in this report. The U.S. has regulatory definitions of wetlands that should be us ed as these definitions have beenResponses to Charge Questions

8 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE peer reviewed innumerable times. Riparian is more a term of art than science. The classical definition is that it includes areas adjacent to flowing w ater, i.e., streams. I’m not sure how floodplains differ from riparian areas, or how riparian ar eas are defined or bounded. The overall report needs an ending synthesis, not summary at the end of the document. The example provided for Southwestern streams, the San Pe dro river is not a representative stream. Much attention has been paid to the San Pedro, m aking it the most studied stream in the SW because it is unique. It flows north from Mexico, has many perennial reaches, almost all of the river has shallow ground water, and mo st has well developed riparian forests. In contrast most streams in the region are ephe meral, few are intermittent and only a very few are perennial. Few have shallow ground water. I would suggest that if the San Pedro is retained, than a second example system is prese nted. One of our published papers (Shaw and Cooper 2008) published in the Journal of Hydrology may pro vide a different representative ephemeral stream baseline. I have attached this in case EPA authors wish to use this or have not seen it.

CLASSIFICATION: I think that a classification of U.S. wetlands would be helpful as a unifying theme for the document. There are many attempts to classify wetlands and regions including EPA’s ecoregion concepts from Omernick et al., i n its many documents. Each region has distinctive wetland types, and it would be nic e to discuss each type and issues related to connectivity, and functions that effect downstrea m waters. In addition, the book on Wetlands of the U.S. should be published this spring/summer by University of California Press. The wetland types or chapters withi n could also provide a good framework for discussing issues related to connectivity, and uncertainty in connections and ecological functions. Another potential is to organize ar ound HGM wetland types, such as depression, slope, etc. although there is great variance t hrough the U.S. on how basin/depression wetland function. Beavers are a key part of the biotic/hydrologic connection fo r streams and riparian areas throughout the northern hemisphere, and even the southern hemis phere. It would be important to mention this important driver of connections and exchange of water, materials and biota between streams and wetlands. I also ask EPA to remove concepts suggesting that riparian a reas are “transition zones”. This is completely false and misleading. Riparian zones suppo rt distinctive biota, hydrological and ecological processes that distinguish them from uplands or aquatic ecosystems. The concept of “channel origin wetlands” is quite foreign. I think that EPAs concept was that sites of ground water discharge would support wetla nds that would feed into downstream waters. However, hydrologically, many wetlands ar e flow through, with ground water flowing in, and ground water flowing out, and no surface water other than in the wetland. This concept is important for the prairie pot holes, but also anywhere else that basin wetlands are prevalent. Many figures could use revision as listed below: Figure 3-2, does not show ground water flow, and little of t he landscape is connected to the channels.Responses to Charge Questions

9 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE Figure 3-7, panel a shows a stream that virtually dries up, and it’s not very representative for perennial streams in most of the US.
Figure 3-6, all of these panels show a river connected via ground w ater inflow. Please expand these concepts to include rivers that are not connected to adjacent lands via ground water. Either they are losing, or disconnected. Same comm ent for Figure 3-13 and Figure 3-16. Figure 3-5, the scale on this is very poor. For example showin g a regional GW flow that is just a tad different from local or intermediate GW flows is inaccurate.

Dodds This report is generally very well written. It clearly makes the case for connectivity of both

streams and wetlands to downstream waters based on many publi shed sources of information. I particularly like the framework of source, sink, refuge, transformation and lag to identify key functions. This approach really allow s the issue at hand to be very clearly explored. However, this framework is not really c learly delineated throughout the document, and I think the document would be strengthened by s ome slight reorganization along these lines.
In a broad sense, the document indicates that the burden of proof should be on those claiming a stream or a wetland is not connected to downstre am waters. The verbiage on lines 5617-5623 is a good example of this concept and potential pro blems with assuming lack of connectivity.

Richardson This is a very nicely written and comprehensive document . The regulatory context is

explained very well as background to understanding the intent of the report. The definitions of terms such as riparian, wetland, connection, et c., are given so that the details are explicit. The case studies approach to giving explicit exa mples and how their connections would be interpreted is a good idea and very ef fective, especially given that the examples were for systems that could be questioned abo ut their connectedness with navigable waters, depending upon interpretation of the terms of the legal opinions. The figures are effective in illustrating principles and evide nce. The conceptual framework with source, sink, lag, transfo rmation and refuge (Leibowitz et al., 2008) is a nice idea, and it provides a good way to educa te readers about the kinds of processes, and how they are influenced by spatial scales and temporal scales. However, this framework doesn’t seem to be used throughout the stream exampl es (chapter 4). For instance, the example from the prairie streams doesn’t ment ion these conceptual components much. The examples given about streams provide good exam ples demonstrating the processes that connect the small tributaries to downstream reaches, but it would be useful to better link these with the conceptual fr amework. The wetland chapter (5) does a better job of bringing these model terms into the desc ription throughout that section. A “non-riparian” wetland (NRCWs – non-riparian and channel origin wetlands) seems an odd term, but I wonder if non-floodplain wetland might be better? The definition of riparian area as transitional between aquatic and terr estrial (P.26) makes it difficult to know when one might no longer be in transition across a floodplai n, for example. Gregory et al.’s (1991) definition of riparian area would make it difficult to have a non-riparian wetland,Responses to Charge Questions

10 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE unless this simply means not in the riparian area of a n avigable-in-principle stream. The consistent use of floodplain and riparian as a combination te rm (e.g., L.590) makes me think that floodplain might be sufficient (later in Chapter 5 the use of “riparian/floodplain” makes them seem interchangeable). Chapter 5 appeared confusing as to whether wetlands were floodplain/riparian (P.212) or NRCWs at some points, but maybe these were to apply to all wetlands. At one point (L. 594) it says that both f loodplain and NRCWs could be geographically isolated, but I am having difficulty seeing how this definition of surrounded by uplands could apply to floodplain wetlands.
It seems like the methylation of mercury is better explaine d on P.233 than it is earlier in the chapter when mercury is discussed for NRCWs. Perhaps the explanation could be moved up to provide the detail when it is first mentioned.
Coastal streams entering the oceans, and not a naviga ble-in-principle river, might not be covered under the definitions used in this report.
Some sections seem to convey a lot of information that is somewhat peripheral to the issue at hand, for instance, it is not clear what the mate rial on P.136-137 contributes to the understanding of whether this is a navigable-in-principle stre am or tributary to a navigablein-principle stream.

It wasn’t clear what the distinction between Carolina Bays and Delmarva Bays is, or whether it is solely geographic. The Glossary did not help w ith that.
It appeared to me that the Executive Summary was a littl e long, depending upon who the anticipated audience for this might be. There is a lot o f territory to cover, and perhaps the regulators will need this much information. The summary is sound, so I am not criticizing the content, just the length.
I am still a bit vague on the opinion of the other 4 justices that were not included in the Scania or Kennedy statements. I think that the other opini on(s) should be explained a little further.
I like the idea of proportional benefits from non-navigable wa ters, as expressed in the Leibowitz et al. (2008) paper. Moreover, the idea that these be nefits may be realized or potential benefits is a helpful way to think about the capa city of a source system to provide benefit. However, these benefits may not be linear with respe ct to concentration or rates in their contributions. For instance, some nitrogen released t o downstream would be beneficial, whereas too much would be detrimental, and the relative benefit might vary in a way that not add up so nicely.
Some authors, such as Stan Gregory (Oregon State U), are t rying to discourage the use of “large woody debris” (L.1780), and in preference use “large wood” to avoid connotations
of waste material given what we know about the important ge omorphic and cover roles of large wood in streams and wetlands.
The “Draft guidance ...” document appears to be for field s taff, and perhaps a decision tree or flow diagram might be useful to distinguish classes of entities and then refer from that to detailed guidance. It seems like a hefty document to plow t hrough to determine what kindResponses to Charge Questions

11 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE of system they are looking at. Of course, all the document is needed, but some way to sort through it quickly might be helpful.

Editorial: L.3135 – change “particularly” to “particular” L.4929 – family Chironomidae, not subfamilyResponses to Charge Questions

12 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE 

### 1. This report concludes that all streams, regardless of flow duration or size, are physically, chemically, and biologically connected to rivers; and these connectio ns, individually or cumulatively, exert a strong influence on the character and functioning of d ownstream waters.

a) Are these conclusions supported by the scientific evidence?

Reviewer Comments
Cooper The conclusions are supported in part. Clearly if hazardous waste is placed into an

ephemeral desert stream, the material will likely flow t o a water of the U.S. on some time scale, likely years to decades.

Crumpton The conclusion that all streams are physically and chemica lly connected to rivers is well

supported if we incorporate a minor modification that seems consistent with the body of the report. Specifically, it is possible to have losing s treams that are not hydrologically connected to downstream waters via channels and perhaps not chemically or biologically connected. I infer this as the basis for the report exclud ing certain channel origin wetlands that feed losing streams. The exception of certain wetl ands spilling to losing streams as potentially not being connected to downstream waters is int roduced in the Executive Summary on page 13, lines 285-289 and repeated numerous times throughout document.

With the exception of certain losing streams that may la ck a connection to downstream waters, the conclusion that at least collectively stre ams exert a strong influence on the character and function of downstream waters is well suppor ted. The report illustrates this through estimates of the fractions of river flow and mate rial loads (nutrients, carbon, etc.) that originate in streams. The report provides sufficient coverage of the relevant pee r-reviewed literature on physical and chemical connections of streams to downstream waters w ith the possible exception of losing stream reaches (i.e., the possible isolation of lo sing reaches from downstream waters). Given the apparent inference in the report that certain losing stream reaches may not be connected to downstream waters, this particular concept should be clarified and supported with relevant literature. In general, the literature was cited and summarized appro priately. The report does a particularly good job in summarizing the complex nature of st ream networks including the major components and their spatial and temporal dynamics

. I offer no response with respect to the questions involving biological connections of streams to downstream waters as this is outside my area of expertise.Responses to Charge Questions

13 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE Cummins The conclusions are supported by the scientific evidence.

Dodds For the most part, these conclusions are supported by the s cientific evidence. There are a

very few cases, where streams flow from wet areas (e.g., mountains) into dry areas (e.g., deserts), where streams might not connect to any downstream waters. However, these sites are the exception, not the rule.

La Baugh Note: underlined text identifies critical or e ssential suggestions.

The general synthesis of the cited literature provided in the report supports conclusion 1. The document, however, includes some conceptual inconsistencie s that would benefit from resolution and clarification. These items are noted below

.

• Page 30, lines 634 to 635 – Figure 3-5 – Because the wetland is at a location where there is a break in slope, the absence of groundwater in teraction with the wetland is remarkable. The fact there are local, intermediate, an d regional flow systems is illustrated by Toth’s work [see figure A-4 in Winter e t al. (1998) http://pubs.usgs.gov/circ/circ1139/pdf/circ1139.pdf ]. Other figures in Winter et al. (1998) provide cross section diagrams of flow to rivers that i ncludes arrows for local and regional flow, such as for a riverine valley – Figure 22 on page 39.

• If the intent of the use of a figure in this part of the introduction, however, is to indicate flow from groundwater follows shallow, intermediate, and de ep flow paths prior to discharge to a river, each representing different amount s of time in transit, a better figure would be something like Figure 3 from Winter et al. (1998). An additional reference for the fact that groundwater representing diffe rent flow paths and times in transit discharge to a stream is Modica, E. 1999, Source an d age of ground-water seepage to streams. U.S.Geological Survey Fact Sheet 063-99, 4 p. http://pubs.usgs.gov/fs/1999/0063/report.pdf

• Page 33, lines 680 to 682 – Are all alluvial aquifers referred to as hyporheic zones? The parenthetical statement equating hyporheic zone with al luvial aquifer is problematic. To avoid confusing readers, the statement equat ing hyporheic zone with alluvial aquifers could be deleted.

• Page 38, lines 768 and 769 – The phrase “aquifers contract” is unusual. Does the formation that is capable of conducting groundwater contrac t? Perhaps what was meant was that groundwater levels decline.

• Page 42, line 826 – The phrase “This water has can alter the geomorphology...” i s awkward. Revision for clarification would be useful.

• Page 62, line 1195, and page 63, Figure 3-17 – Use of the term ‘impermeable aquifer’ is incorrect.
An aquifer by definition is “A body of rock that contains suff icient saturated permeable material to conduct ground water and to yield economically significant quantities of water to wells or springs.” Margret Gary, Robert McAfe e Jr., and Carol L. Wolf, editors, 1972, ‘Glossary of Geology’, American Geological Institute, W ashington, D.C.; or “AnResponses to Charge Questions

14 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE aquifer is a formation, group of formations, or part of a formation that contains sufficient saturated permeable material to yield signific ant quantities of water to wells or springs.” S. W. Lohman and others, 1972, Definitions of sele cted ground-water termsRevisions and conceptual refinements, U.S. Geological Survey Water-Supply Paper 1988, 21 p.

• Page 62, lines 1194 to 1200 – It would be useful to revise the paragraph to clarify t he key points being made about flow systems while being consisten t with correct use of technical terms. It is not at all clear why the explanat ion includes reference to intermediate or regional flowpaths. Intermediate and regi onal flow paths occur as a function of groundwater basin depth to width ratio (Toth, J.A., 1963, A theoretical analysis of ground-water flow in small drainage basins. Journal of Geophysical Research, v. 68, p 4795-4811). Also, surface waters with low pe rmeability deposits in area of high topographic relief can receive water from be yond the local surface watersheds (Winter et al., 2003, Where does the groundwater in small watershed come from? Ground Water, v. 41, p. 989-1000).

• Page 135, line 2731 – Because vagility has the same meaning as capability of movement, is there any reason to use the term? Consider del eting vagility to simplify the text.

Rains SUMMARY

The conclusions are supported by the scientific evidence provided . This is the easiest task for the authors, because hydrological and ecological connectivity are fundamental tenets for these systems. However, I do have comments regarding s ome flaws and/or inadequacies in the scientific evidence provided as justifica tion. (See, also, the detailed comments related to the conceptual framework in the section titled “Additional Reviewer Comments” below.)

DETAILED COMMENTS
General Comment: There is incomplete discussion of perennia l tributaries that are disconnected from perennial mainstems by seasonal or ephemera l reaches. This commonly occurs in the West, where tributaries are often perennial in the mountains but lose rapidly and are intermittent or ephemeral on the alluvial fans (Izbicki 2007). Furthermore, there is no discussion at all of closed basins that lack any kind of navigable water at all. I don’t know about now, but I do know that a few years ago, the U.S. Arm y Corps of Engineers (Corps) Albuquerque District was calling these isolated ba sins not subject to federal jurisdiction under the Clean Water Act (Parenteau 2004-2005). This document should provide clearly articulated evidence, one way or another, to ward connectivity in these contexts to better enable decision-makers to resolve this pol icy conflict. Nadeau and Rains (2007) foresaw this, and separated this case out for special attention. Something like that might be called for here, too.

l. 1492-1537: This entire section would be greatly strengthened if you would include a review of some of the papers that show that hydrological a nd ecological connectivity are central tenets of stream hydrology and ecology. Some examples might include the Four-Responses to Charge Questions

15 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE Dimensional Nature of Lotic Ecosystems (Ward 1989), the Ri ver Continuum Concept (Vannote et al., 1980), the Serial Discontinuity Concept (Sta nford et al., 1988, Ward and Stanford 1995, Stanford and Ward 2001), and the Featured Coll ection of JAWRA devoted to this very topic (Nadeau and Rains 2007 and references ther ein; Note: The Nadeau and Rains 2007 referenced in this specific instance is differ ent than the Nadeau and Rains 2007 referenced throughout the document and elsewhere in this revi ew. See Additional Literature Cited below.). Doing so will accomplish two objectives: (1) make it clear from the outset that we’ve long since accepted hydrological and ec ological connectivity as fundamental tenets and (2) provide critical context for much of the remaining discussion of the specific examples (e.g., l. 2174-2175).
l. 1517-518: This sentence is redundant with the following paragr aph. I suggest omitted this sentence here altogether, and relying entirely upon the following paragraph to make the point.
l. 1697-1698: Water scours channels, not sediments. l. 1698-1701: Add “reducing channel capacity” to the list. l. 1710-1716: Lane (1955) is an excellent way to understand and expl ain reach-scale flowsediment dynamics. Because Lane (1955) is often difficult to t rack down, you might also cite Bull (1991), who republished the findings of Lane (1955).
l. 1977-1978: The following two comments relate to nutrient subsidi es, which you mention, though not specifically by name, elsewhere in the doc ument (e.g., l. 2174-2175). Drs. Dodds and Wipfli may also mention nutrient subsidies. Therefore, you may choose to consider the following two comments here or elsewhere in a se parate paragraph dealing specifically with nutrient subsidies.
l. 1977-1978: You might consider adding a paragraph here on seasonal nitrate fluxes in Mediterranean and other similar seasonally arid environments . Such seasonal fluxes have been repeatedly observed and explained as an asynchrony betw een hydrological and biological processes in annual grasslands in Mediterranean and other similar seasonally arid environments (Tate et al., 1999, Holloway and Dahlgren 2001, Rains et al., 2006). Quoting from the latter: “Upland annual grasses senesce in t he dry season. However, microbial activity continues, nitrogen is mineralized, a nd nitrate accumulates in the upland soils. Annual grasses germinate early in the wet season, but do not develop substantial biomass until the middle- to late-growing season (i.e., Mar ch–April). Thus, during the early-season storm events, there is little biological dema nd for nitrate and it is readily leached from the upland soils into the perched groundwater tha t ultimately discharges to the vernal pools. Later in the wet season, much of the nitrat e in the upland soils has been flushed and the upland annual grasses are flourishing, which prod uces a large biological demand for the remaining nitrate. Therefore, the amount of nitrate leaching into the perched groundwater and subsequently discharging to the vernal pools decreases.”
l. 1977-1978: You might consider adding a paragraph here on alder-fi xed nitrogen subsidies in wetlands and streams. For example, Shaftel e t al. (2010) showed that nitrogen concentrations are correlated with alder cover in salmon- bearing headwater streams on the lower Kenai Peninsula, Alaska. We are now conducting follow up work to determine if allResponses to Charge Questions

16 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE alder patches are created equal in this regard, or if som e alder patches are better positioned to provide these subsidies. l. 1987-2001: There is more literature on this issue that you mi ght consider incorporating here. Triska et al. (2007) did a nice study on the transport and transformation of nitrogen as it moved from a hillslope to a headwater riparian wetland and into and down the headwater stream, with the latter being pertinent in this case. Al so, Hill and Lymburner (1998) and Hill et al. (1998) did nice studies on nitrogen transformation s in hyporheic zones, showing that even short, shallow, and fast flowpaths through the h yporheic zone are sufficient to transform a large amount of the available nitrogen. These studies are all nice compliments to Alexander et al. (2000), which is already described in the document. l.2035-2047: I’ve always thought of spiraling as a form of short- and long-term storage. Nutrients are essential, yet are always in motion towar d the receiving water bodies (e.g., the ocean). Nutrient spiraling is a way by which those nutrien ts are temporarily stored, perhaps for a short time (e.g., algae), or perhaps for a long-time (e.g., trees), before being released again to downstream ecosystems. This is simi lar to the roles played by woody debris and floodplains in the short- and long-term storage of sediments.
l. 2398-2407: You make a good argument, but you might consider adding the importance of upstream migration. I don’t know much about this, but I’m led to believe that invertebrates tend to fly upstream after emergence, all the better to recolonize upstream habitats that tend toward depopulation due to drift. I d on’t know if this actually true— though it seems that it must be true—or of there is any lit erature on this if it is true— though I do recall being told that there is literature on this by someone knowledgeable.
l. 2486-2487: You might consider adding a paragraph here on the impo rtance of anadramous fish in transporting nutrients, especially m arine-derived nutrients, to headwater streams and associated riparian habitats. The re is a good review of this in Nadeau and Rains (2007). l. 2486-2487: You might also consider adding a paragraph here on barr iers and the effects of barriers. Dynesius and Nilsson (1994) showed that 77% of the t otal water discharge of the 139 largest river systems in North America north of Mexico, Europe, and the former Soviet Union are fragmented by dams and/or significant w ater abstraction. Stanford et al. (1988), Ward and Stanford (1995), and Stanford and Ward (2001) talked about this in terms of the natural flow of mass, energy, and organisms, terming the overall effect the Serial Discontinuity Concept. And Fleckenstein et al. (2004) provided a good example of this, by showing that groundwater pumping causes a regional gro undwater drawdown, which causes enhanced groundwater recharge through the stre ambed of the Cosumnes River, which causes the cessation of flow in Cosumnes Rive r in the early fall, which creates a barrier to a fall-run Chinook salmon population.

Richardson Yes, the conclusions are consistent with the evidence prese nted in the scientific, peerreviewed literature.Responses to Charge Questions

17 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE Snodgrass Yes, the scientific evidence clearly indicates a significan t influence of physical and

biological processes in streams having a large influence on downstream rivers. Streams provide significant amounts of materials (including nutrie nts, pollutants, sediments, and water) and organisms and control their temporal dynamics and rates of delivery to river systems.

van der Valk Yes. Although I am not a hydrologist or stream ecologist, th is is clearly demonstrated in

the literature cited.

Wipfli Yes, to the best of my knowledge, the conclusions are fully suppo rted by the evidence in

the scientific literature. There is strong evidence in t he scientific literature that headwaters are physically, biologically, and chemically connected to, a nd influence, downstream waters and associated biota. The evidence reported and cited in this review is presented accurately, thoroughly, and clearly.



### b) Does the report include the most relevant peer-reviewed literature on these topics, including evidence of connectivity and isolation? If not please indicate which references are missing.

Reviewer Comments
Cooper See comment 1a) above.

Crumpton See comment 1a) above.

Cummins By and large the report does include the most relevant peer r eviewed literature to address

the question. However I have the following comments and recomm endations. Page Line Comment 2 32 ... spiraling... Unlike standing waters where nutrient cycles ar e closed

loops, the unidirectional flow of streams creates open cyc les in which release of a nutrient is displaced from its uptake site. The open nature of the cycles needs to be made clear at the outset. (Also, 8, 184; 8, 190; and the entire section 9, 191-206 should include the concept that the cycles are open.) 11 253-60 A major feature of dams is to reverse the seasonal hyd rology of streams and rivers on which they are constructed. The purpose of m ost dams is to truncate peak flows in the normal season of high runoff (stor age for dry season release and use) and to increase flows during these normal low flow seasons. This reversal of normal hydrological patterns has immense implications for life cycles of lotic organisms. This point should be made here or elsewhere. 15 342-44 Furthermore... isolated. In fact, some ecologists have sugges ted using airshed, watershed, and ground-watershed to categorize all t he approximately definable inputs and cycles with in a region.Responses to Charge Questions

18 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE 23 509-10 Headwater streams are first- and second-order stream s... I feel strongly

that alternatives to this statement should be acknowled ged. For example, the River Continuum Concept (Vannote et al., 1980, cited 4, 708 ti mes so far) groups first-to third-order streams as those headwa ter streams in which riparian vegetation dominates the in-stream biology. Most or ders one to three have canopy closure sufficient to strongly influence in-stream primary production (designated as P/R <1) and the input of plant litter that is the dominant energy base of stream ecosystem function i n most headwater streams.
Here, and elsewhere, the point should be driven home tha t stream order is a

geomorphic concept and probably never should be inferred from blu e lines on a map, which can represent anything from first-order to fourth-order depending on map scale. In addition, the stream class system of categorizing streams by fish-bearing condition (e.g., Cali fornia Forest Practices Rules, Section 936.4) should be laid to rest. Thi s is not a geomorphic defensible classification and should be permanentl y discouraged. [“Class I watercourses are defined as fish always or seasonally present onsite, including habitat to sustain fi sh migration and spawning. Class II waters are defined as 1) fish always o r seasonally present off-site within 1000 feet downstream and/or 2) aquatic habitat for non-fish aquatic species. Class III watercourses do not ha ve aquatic life present” (This is impossible at all seasons and in all years – e.g., aquatic Diptera, appear within days of flooding of forest access r oads) “and are capable of sediment transport to Class I and II waters u nder normal high water flow conditions. (Cummins, K. W. and M. A. Wilzbach . 2005. The inadequacy of the fish-bearing criterion for stream manage ment. Aquatic Sciences. On line; http://www.birkhauser.ch , pp 1-6). 24 531 ...symmetry ratio... another way is link number, which sums t he total

number of first-order tributaries entering a watershed of a given order. Fig. 3-1 shows no first-order tributaries entering directly int o the third-order mainstem which would be quite unusual. Link number is a useful measurer for stream ecologists working at the watershed scale bec ause the first-order tributaries are those in which the riparian influence on in -stream biological community composition and productivity is maximized. 26 559 Fig. 3-3. The diagram’s horizontal bars give no indicati on about the

massive controversy about the width of riparian areas. This point is the major element of all forest practice rules, including the sentinel Northwest Forest Plan that defines the width in terms of tree hei ght in the riparian area. The point that needs to be acknowledged (driven home), is that stream ecologists, fisheries managers, and forestry mana gers all have different concepts (or biases) about the definition of the wid th. For example, stream ecologists may focus on the width necessary to provide the width that supplies plant litter that constitutes the pr imary energy source of headwater stream ecosystems, fisheries manager s are concerned with the width necessary to insure the input of large wood whi ch is theResponses to Charge Questions

19 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE

mainstay of fish habitat in streams and rivers in genera l, and forestry managers are concerned with how much width will be exclude d from harvest by almost all forest practices rules. So, for s cientific, Endangered Species Act, and economic reasons defining the width or the c riteria for defining the width of the riparian zone is far from a trivial matter. At least replace the end bars on the riparian widths in Fig. 3-3 wit h a dashed line at the ends. The figure caption should explain that the dash l ines indicate that the boundary of the riparian zone depends upon the function being considered (e.g., Gregory et al., 1991). 51 1000 Figure 3-14). Also, dissolved organic matter (DOM) forms complexes with

divalent cations, primarily Ca, converting DOM to fine part iculate organic matter (FPOM, particle size < 1mm) and is taken up dire ctly by benthic bacteria. This significantly delays the export of organic m atter down river. DOM almost universally accounts for 50% of all the organic matter in transport in all order streams (Vannote et al., 1980 and t he Minshall et al., River Continuum publications). This retention of FPOM, rathe r than loss as DOM, has major consequences for stream and river i nvertebrates and is likely a major factor in the productivity of hard water ( calcium rich) streams. 80 1484 Swanson et al. (1987) suggest that short recurrence inte rvals involve flows

too small to cause significant changes in stream channel ge omorphology, and very long recurrence intervals cause very major alter ations in channel form, but the intermediate recurrence intervals are the events that have the major effects in shaping the current condition of most cha nnels.[Swanson, F. J., L. E. Benda, S. H. Duncan, G. E. Grant, W. E. Megahan, L. M. Reid, and R. R. Zimmer. 1987. Mass failures and other processes o f sediment production in Pacific Northwest forest landscapes. Pp. 91 -138 in : Salo, E. O. and T. W. Cundy. (eds.). Streamside management: fores try and fisheries interactions. Institute of Forest Resources, Univ. Washi ngton, Seattle. (If the NRC publication is cited, this one should be eligible as well; it was reviewed by outsiders.)]
108 2106 Cite Cushing et al. (eds.). 2006. This 817 page volume includes chapters

by worldwide authors on streams and rivers of North Ameri ca, Central and south America, Europe, Africa, Asia, Australia and New Zealand, and Oceana. The editors charged the authors with using data fr om streams and rivers in their respective regions and comparing it with the River Continuum Concept (Vannote et al., 1980). The comparisons are about linkages (connectivity) between headwater streams and large rivers on a world wide scale. The introduction by the editors presents a n overview of stream ecosystems. The River Continuum Conceptual Model (Vanno te et al., 1980) is reproduced in the Introduction. This is the mode l that relates stream/river ecological structure and function to the position along the downstream trajectory. (Cushing, C. E., K. W. Cummins, an d G. W. Minshall. 2006. River and stream ecosystems of the world. Univ.Responses to Charge Questions

20 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE

California Press, Berkeley 817 p.) 110 2145 ...108 m for whole leaves... This compares to the 100 m in Cummins e t al.

(1989) and not to the 1000 m cited in this report. 112 2197 ...snow melt. Approximately 50% of transported carbon was D OC in all

streams (orders 1-8) covered in the River Continuum studies ( Vannote et al., 1980, Minshall et al., 1983, 1992). 112 2206 ...river network. An important point here is that anaerobi c storage of

CPOM, e.g., leaf litter, greatly delays breakdown of CPO M to FPOM in the absence of hyphomeycete fungi and shredders, both of which ar e obligate aerobes (Cummins et al., 1980. [Cummins, K.W., G.L. Spengler, G.M. Ward, R.M. Speaker, R.W. Ovink, DC Mahan, and R.L . Mattingly. 1980. Processing of confined and naturally entrained leaf litt er in a woodland stream ecosystem. Limnol. Oceanogr. 25:952-957.] 120 2382 Wilzbach and Cummins (1989) demonstrated a higher % mortali ty among

drifting individuals than their benthic counterparts. Thi s raises the possibility that a significant amount of invertebrate str eam drift is destined to have no impact on downstream colonization of invertebrates, with the primary effect being the contribution being to the downstream de trital suspended load. (Wilzbach, M. A. and K. W. Cummins. 1989. An assessment of short-term depletion of stream macrobentho s by drift. Hydrobiologia 185: 29-39. 146 2970 ...gatherers, the dominant group... the term is defined, but as in the case of shredders (which was not defined or referenced when used) no citation is given. There are a great many that could be used, e.g., Cummins 1974, Cummins and Klug 1979. [Cummins, K.W. 1974. Structure and function of stream ecosystems. BioScience 24: 631-641; Cummins, K.W. and M.J. Klug. 1979. Feeding ecology of stream invertebrates. Ann. Rev. E col. Syst. 10:147-172; the designations are also part of the River C ontinuum Concept.] 148 3002 ...reaches 500 and 1,000 m upstream. Distance traveled by the ma jority of introduced leaf litter in a forested second-order stre am by reported to be about 100 m by Cummins et al. (1989). [Travel distance of lea f litter was reported from the time the litter is wetted. Senescent G inkgo leaves were used in these experiments; they are bright yellow and remai n so for several weeks because they are very resistant to biological processi ng. Also, the leaf shape is unlike any of the native riparian tree species in eastern headwater streams.] Attached is a figure that might be of interest to some p eople at the meeting. I make no suggestion whatsoever that this Figure should be any part of t he report. It is merely a “snap shot” offered in support of the argument that I did make i n the report about including more detail on one of the sentinel features of connectivity betwee n riparian vegetation and structure, function and productivity of invertebrate populations in headwater streams (which I would define as first- to third-order). The photog raph is not unique; this sort ofResponses to Charge Questions

21 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE picture could be taken of leaf litter from any stream in the world during any season when riparian plant litter is available in streams (including intermittent channels). I have such pictures from streams in southern and northern California, O regon, New Mexico, Yellowstone Park (Wyoming and Montana), Idaho, Michigan, Penns ylvania, Maryland, Florida, Sweden, Denmark, Italy, Australia, New Zealand , Brazil, and Guinea West Africa.

Fig. A. Conditioned red alder leaf eaten by caddisf ly (Trichoptera) larvae. Note: better conditioned ( higher aquatic hyphomycete fungal biomass) soft tissues eaten in p reference to the poorly conditioned midrib and majo r veins which are high in lignin. (Cummins et al., 1989).
Just for background information. A companion to the comment at page 146, Line 2970, Response to Techni cal Charge Question 1.

So, as I argued in one of my comments in Response to Charg e question 1, this world wide and highly predictable connection between riparian vegetation a nd in –stream biology is worthy of more than the undefined use of the term “shredders” which occurs at a single place in the report. There are over 1,000 references in the literature that address this example of connectivity.

Dodds This report is well referenced. There are so many refe rences on this subject, that it would be impossible to include them all. The document however, doe s cite plenty of references that clearly illustrate the main points of the report.Responses to Charge Questions

22 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE La Baugh A useful reference regarding the interaction of streams and groundwater is absent from the

references – Jones, J.B., and Mulholland, P.J., eds. 2000. S treams and Ground Waters, Academic Press, 425 p.

Rains See comment 1a) above.

Richardson The authors provide a comprehensive suite of references to support their summary and

conclusions. These references are the most relevant, and other papers that come to mind would not further enhance the understanding of the topic. One that deals with the punctuated delivery of large wood to channels and its storage and lag processes is by Swanson et al. (1998).
Swanson, F.J. et al. 1998. Flood disturbance in a foreste d mountain landscape - Interactions of land use and floods. BioScience 48:681-689.

Snodgrass Although the report is focused on influences that move from upstream to downstream (as is

clearly stated in the report), some degree of isolation of headwater streams is important for the biological integrity of these habitats. For example, s ome species of stream-side salamanders are headwater specialist, which are only found i n large numbers in headwater streams (Snodgrass et al., 2007; Peterman et al., 2009). Headwa ter specialists often have adaptations that allow them to cope with desiccating conditi ons that limited the development of predator populations (Meyer et al., 2007). Many insects as well as other invertebrate taxa are also endemic to headwater streams (e. g., Dieterich and Anderson, 2000; Fend and Brinkhurst, 2000; Fend and Gustafson, 2001). Therefore, protection of the isolated nature of headwater streams is also an importa nt component of protecting the biodiversity associated with our nation’s waters. The aut hors do acknowledge these ideas (see lines 906-907; 1020-1022), but I feel they are also important f or managers and policy maker to appreciate. If the main focus of the report is t he emphasis of effects on downstream waters, then more detailed treatment of the influence of connectivity on upstream headwaters and wetlands may not be warranted.
Although not crucial to demonstrating the influence of headwa ter streams for downstream rivers, in the sake of being complete it is probably worth noting the role of beavers in the functioning and influence of headwaters on downstream rivers . Beavers can dam extensive lengths of moderate to low gradient headwater streams (e. g., Snodgrass 1997), greatly altering their hydrology and geomorphology (Pollock et al., 2003; B utler and Malanson, 2005) and provide habitat for numerous organisms (e.g., Snodgra ss and Meffe 1996; Stevens et al., 2006). These hydrological and geomorphological cha nges have large impacts on ecosystem function (Naiman et al., 1996) includin g greatly increased rates of denitrification (Naiman et al., 1994). Additionally, beaver pond s can be areas of high rates of mercury methylation (Roy et al., 2009). These points rela te to the idea of headwater streams being places of lag and transformation. This ma terial should be added as the wetlands that beavers form would fall into the floodplain /riparian category of wetlands.
When the authors discuss mapping issues for headwater stream s (lines 1519-1530) they should include the Brooks and Calhoun (2011) reference; they migh t even include some numbers from this publication. Specifically, Brooks and Calho un (2011) estimate that 21%Responses to Charge Questions

23 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE of 400.3 km of stream did not show up as blue lines on 1:25,000 scale US GS topographic maps. There is also the issue of channels that were for med under past land use scenarios that currently do not ever hold flowing water. Although the def inition of “stream” includes flowing water (lines 503-504) later the authors suggest that hea dwater stream originate at where “runoff is sufficiently concentrated to erode a defi nable channel” (line 518). Some clarification should be included to make it clear that there are two components to a stream: flow at some time during the year and the formation of a c hannel.
On lines 3399 through 3413 the authors summarize the effects of al tered flow regimes on invasiveness of native communities. Meffe (1984) should probabl y be cited here as this is one of the original, if not the original, documentation of the influence of natural flow regimes on co-existence of native and introduced fish species. Additionally, the bullet on line 3434 should include the prevention and/or mitigation of the effects of invasion by introduced species. Again, this is a place to integr ate the balance between lag and source and how their alteration can impact downstream rivers.

van der Valk Again, I am not a hydrologist, this review, however, cites a large number of relevant

references to document the connectivity of streams to ri vers. I doubt that any additional references would in any way alter the conclusions drawn.

Wipfli Yes, to the best of my knowledge, the report includes a broad , relevant literature on the

connections between headwaters and downstream freshwater ec osystems. However, I did not see literature discussed and cited that addresses t he linkages between headwaters and estuaries and oceans, even though that point is stated in th e first paragraph of “Background” section of “Technical Charge to External Peer R eviews” document. Should this be included? Five additional references from my headwaters work on biologica l linkages that may be helpful are listed below. The latter four deal with manage ment effects on headwater streams. Wipfli, M.S., and C.V. Baxter. 2010. Linking ecosystems, f ood webs, and fish production: Subsidies in salmonid watersheds. Fisheries 35(8): 373-387. This paper takes a broader look at watersheds, putting into context the biological connections between headwaters, river networks, riparian habitats, and the ocean.
Binckley, C., M.S. Wipfli, R.B. Medhurst, K. Polivka, P. Hessburg, B. Salter, and J.Y. Kill. 2010. Ecoregion and land-use influence invertebrate and de tritus transport from headwater streams. Freshwater Biology 55: 1205-1218. This paper shows how past timber harvesting affects invertebrate flow from headwaters to downs tream habitats.
Medhurst, R.B., M.S. Wipfli, K. Polivka, C. Binckley, P. Hessburg, and B. Salter. 2010. Headwater streams and forest management: Does ecoregional context influence logging effects on benthic communities? Hydrobiologia 641: 71-83. Addresses past timber harvest effects on headwater stream invertebrate communitie s. Wipfli, M.S. and J. Musslewhite. 2004. Density of red alder (Alnus rubra) in headwaters influences invertebrate and organic matter subsidies to down stream fish habitats in Alaska. Hydrobiologia. 520: 153-163. This paper showed that headwater streamsResponses to Charge Questions

24 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE also supply terrestrial invertebrates to downstream waters, in add ition to aquatic invertebrates, and illustrated how riparian management affects biological connections between riparian areas, headwater streams, and downstream water s. Piccolo, J.J., and M.S. Wipfli. 2002. Does red alder (Alnus rubra) along headwater streams increase the export of invertebrates and detritus from headwa ters to fish-bearing habitats in southeastern Alaska? Canadian Journal of Fis heries and Aquatic Sciences. 59: 503-513. This paper looks at how riparian regrowth following timber harvest in Alaska affects transport of aquatic invertebrates to downstream waters. Another paper from research we conducted on headwater stream s looking at the role of wildfire in affecting linkages between headwater streams and downstream waters, via the flow of invertebrates downstream: Mellon, C.D., M.S. Wipfli, and J.L. Li. 2008. Effects of forest fire on headwater stream macroinvertebrate communities in eastern Washington, USA. F reshwater Biology 53: 2331–2343.



### c) Was the reviewed literature cited and summarized correctly? If not ple ase indicate where correction or revision is needed.

Reviewer Comments
Cooper See comment 1a) above.

Crumpton See comment 1a) above.

Cummins The Literature that was cited was summarized correctl y.

Dodds Yes, the literature was reviewed and cited correctly. O ne minor addition could be that there

is one reference that is cited, Dodds and Oakes 2006, which indi cates that intermittent streams are connected chemically to larger streams and ri vers even during times of the year when the streams are not flowing. This point is not mentioned but is very important to the issue of connectivity.
I found the illustrative materials in this section quite useful and well done. However, I would like to see the figures such as 3-6 include diagrams of losing stream reaches as well, although figure 3-13 helps. Also a figure with a longitudinal cr oss section indicating hyporheic flow, and how such flow can connect isolated pools during dry periods could also be useful. Finally, Table 3-1 is a bit confusing as i t looks like everything flows into everything else through the river. I would just lose the mult iple italicized words in the first column that say “River”, or space out the individual rows fur ther to make it clear that each row is not linking to the next. I think figure 3-14 is somewhat misleading as it ignores cycling through inorganic forms.
Line 1031, these streams flow during and immediately following pr ecipitation.Responses to Charge Questions

25 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE A clearer discussion of when increased connectivity can be bad (e.g., introduced species) might be useful. The information was in the document, but bu ried. (e.g., at line 1408).
Line 1772, confluences are not “much like dams”, they can ch ange longitudinal patterns, but much less severely and in very different ways from dams

. Line 1793. In the Flint Hills of Kansas, wood does not accumul ate in small streams, and such streams are an important source of large wood to down stream rivers. This wood is very important habitat as well as a geomorphologic force i n rivers. This statement might need to be qualified a bit. Line 2495, might want to discuss the Falke and Gido 2006 (in refere nces) work here on reservoirs disconnecting small streams from each other. Line 2560. This could be stated more strongly. The evidence uneq uivocally demonstrates connectivity between streams and downstream rivers.
Line 2589. Work of Alexander et al. (2000) and Mulholland et al. (2008) , Woolheim et al. (2008) both explicitly examine movement of materials along river network. This reference is also important Helton, A.M., Poole, G.C., Meyer, J .L., Wollheim, W.M., Peterson, B.J., Mulholland, P.J., Bernhardt, E.S., Stanford, J.A., Arang o, C. & Ashkenas, L.R. (2010) Thinking outside the channel: modeling nitrogen cycling in networke d river ecosystems. Frontiers in Ecology and the Environment, 9, 229-238.

Line 2718. The fact that nutrients are elevated in most e coregions, and these are generally related to non-point source land use characteristics, is highly indicative of stream connection. Dodds, W.K. & Oakes, R.M. (2004) A technique for es tablishing reference nutrient concentrations across watersheds affected by hu mans. Limnology and Oceanography Methods, 2, 333-341. Line 2750, these are still net heterotrophic, so they are der ived to a lesser degree than forested areas. Line 3059, this pattern was also probably driven by bass in the impoundments. Figure 4-9 the title is wrong.

La Baugh • Page 42, line 828; page 175, line 3579; page 307, line 6921 – The name Meybloom in

the citation is incorrect. Correct name for this cita tion is Meyboom

.

• I am not familiar with all of the literature cited in the document regarding the relation of streams to their connection with and influence on downstream rivers, therefore I am not able to judge whether or not all of the cited literature was summarized correctly.

Rains See comment 1a) above.

Richardson The review provides a solid assessment of the literature a nd covers the evidence for

connections. Yes, the conclusions are supported and appropriate li terature is compiled. The authors have been careful throughout to point out any uncer tainties in the conclusions that can be drawn from the available literature. The only limit ation to the assertion that allResponses to Charge Questions

26 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE streams are connected to rivers might be in the case of c oastal streams not contributing to a nexus with a navigable-in-fact river, but these are still connected to streams (or estuaries) downstream.

Snodgrass In general, the literature interpretation is correct and the literature cited extensive. I have

only a few minor comments here. On lines 2412 through 2414 the autho rs suggest that most fishes utilizing headwaters can also be found further downstream and cite Horitz (1978). This may be true for more species poor assemblages, but in more species rich areas it is common to find species of fish confined to headwater s treams. See discussion above for references. This change should be made in the final do cument.

van der Valk I am not an expert on hydrology, but I did not find any obvious pr oblems with literature

citations or with the interpretations of the literature.

Wipfli Yes, the literature in this report was cited and summari zed accurately. The authors

provided a very clear and thorough illustration of the demonst rated linkages that connect headwaters to downstream waterways. A few points that might help:

Line 1494 – “and associated biota” at the end of the sentence? Lines 1698, 1709, 1844 – Several places in the text (these two as exam ples) could benefit with a relevant citation.

Lines 1793-4 and 1804-6 seem to be in conflict with each other. Line 2160 – space before 100. Line 2375 (whole section) – this would be a good place to discuss the role of terrestrial invertebrates that enter headwaters, and in turn get trans ported downstream from headwaters (Wipfli and Musslewhite 2004). Not sure if the autho rs would like to have this concept in the report, but it also ties in human impacts into the story.Responses to Charge Questions

27 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE 

### 2. This report concludes that open water and wetlands in riparian are as and floodplains of streams and rivers are physically, chemically, and biologically connected w ith the river network, and that their functions exert a strong influence on the ch aracter and functioning of downstream waters.

a) Are these conclusions supported by the scientific evidence?

Reviewer Comments
Cooper The report provides evidence of these connections, but what is missing is some idea of how

often and how long these connections must occur each year. I wou ld also like to see a better review of the types of channels and wetlands that o ccur in the U.S. and which we have sufficient evidence for these connections, and which w e don’t. This could be presented in a table.

Crumpton The conclusion that wetlands in riparian areas and floodpl ains of streams and rivers are

physically, chemically, and biologically connected with the ri ver network is well supported by the scientific evidence (with the possible exception of w etlands in riparian areas and floodplains of certain permanently losing steams that ar e never connected to downstream waters- these systems would be rare). The report ill ustrates this through literature documenting the unidirectional and bidirectional transfer of water and materials and transport and migration of organisms. The conclusion that wetlands in riparian areas and floodpl ains of streams and rivers exert a strong influence on the character and function of downstr eam waters is well supported by the scientific evidence – at least for the systems coll ectively, and that qualification should be included in the conclusion

. The report provides sufficient coverage of the relevant pee r-reviewed literature on physical, chemical connections of wetlands in riparian areas and floodplains to the stream networks. The literature was cited and summarized corr ectly. The report recognizes the uncertainty in quantifying exchanges between stream/ river channels and their riparian areas/floodplains and provides sufficient documentation of the t ransfers without extending the analyses beyond what can be reasonably concluded.

Cummins The conclusions are supported by the scientific evidence.

Dodds Yes, these conclusions are supported.

La Baugh The general synthesis of the cited literature provided in the report appears to support conclusion 2. Part of the text pertaining to the relation of open water and riparian wetlands to streams and rivers would benefit from clarification, a s noted below.

• Page 2, lines 38 and 39 ; page 10, line 225 – The phrase “...storage of local groundwater sources of baseflow in rivers,” could benefit from clarification. Was the intent of the text that riparian and floodplain wetlands a re areas where groundwater flows to the wetlands rather than the adjacent river, the reby intercepting groundwater that otherwise would contribute to baseflow?Responses to Charge Questions

28 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE Rains SUMMARY

The conclusions are supported by the scientific evidence provided . This is still a relatively easy task for the authors, because hydrological and ecological connectivity are fundamental tenets for these systems. However, I do have comments re garding some flaws and/or inadequacies in the scientific evidence provided as justifica tion. (See, also, the detailed comments related to the conceptual framework in the section titled “Additional Reviewer Comments” below.)

DETAILED COMMENTS

General Comment: The classification scheme used in this doc ument is unusual. I understand why you might want to separate this into channels , wetlands on floodplains, and wetlands not on floodplains, given the regulatory environme nt. However, this is not a common way to classify wetlands, which makes the document a bit hard to follow. I think that you can leave this general separation in place, but you mi ght then explain what kinds of wetlands might be included, using an HGM classificati on scheme. In this way, you can explain that this chapter is dealing with all kinds of w etlands—riverine as well as flat, depressional, slope, lacustrine, and estuarine—as long as they are subject to regular or episodic flooding and therefore connection to streams. l. 3524-3556: This entire section would be greatly strengthened if you would include a review of some of the papers that show that hydrological a nd ecological connectivity are central tenets of floodplain hydrology and ecology. Some examples m ight include the Flood Pulse Concept (Junk et al., 1989, Tockner et al., 2000) and t he extension of the Serial Discontinuity Concept to floodplains (Ward and Sta nford 1995). Doing so will accomplish two objectives: (1) make it clear from the outs et that we’ve long since accepted hydrological and ecological connectivity as fundamental tenets and (2) provide critical context for much of the remaining discussion of the specific e xamples. l. 3574-3575: You might also consider adding a paragraph here on the role that bank storage plays in supporting baseflow, especially immediate ly following high flows (Whiting and Pemeranets 1997, Hammersmark et al., 2008). l. 3584-3585: Here and in a few other locations, you use the word “filter” to describe sediment removal from flowing water by riparian and floodplai n wetlands. However, it isn’t a filtering effect, it’s a hydraulic effect, as w ater slows, loses strength (e.g., specific stream power), and deposits sediments, usually in order of mass (Meyer et al., 1995, Dabney et al., 1995). You know this to be true, because you go on to say as much later (e.g., l. 3601-3602). This is a little issue; but you’ll forgive me because it’s a pet peeve of mine.
l. 3601: Riparian areas are both sources and sinks for sedime nts. Riparian areas provide both short- and long-term storage locations for sedimen ts, and can be sediment neutral, sediment sinks, or sediment sources depending upon whether the stream has reached its base profile—in which case sediment storage and mobilizati on balance; accommodation space has been created—in which case, sediments can be st ored; or accommodation space has been destroyed—in which case, sediments can be mobi lized (Quirk 1996).Responses to Charge Questions

29 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE l. 3609-3618: This paragraph seems out of place, in that it doesn ’t seem to connect to the surrounding discussion of connectivity, but it will fit much bette r if you broaden the previous paragraph as suggested in my comment titled “l. 3601”.
l. 3644-3646: Groundwater does not always move through the alluvium and /or equilibrate with the temperature of alluvium. Some groundwater that di scharges to riparian environments flows along regional groundwater flowpaths, and is t herefore more likely to have the temperature of the volumetric weighted average of the recharge water (Rains and Mount 2002, Kish et al., 2010). l. 3695-3697: This paper, and a few others, has created a lot of headaches in recent years, because of sentences just like this, which imply that evapot ranspiration causes water levels to rise. The paper, in my opinion, is a bit flawed, in th at it misrepresents the net effect of evapotranspiration and makes a claim wholly unsubstantiated by the data. Let me deal with these issues on at a time. First, evapotranspiration caus es a net decline in water levels, which will tend to move water out of the carbon-rich soils. Hydraulic lift does occur, but that only partially offsets the initial drawdown. Imagine a point just below the water table but in the carbon-rich soils. Before evapotranspiration, t hat point is saturated, so the pressure potential is positive. After evapotranspiration, the water table declines to below that point, so the point is unsaturated, so the pressure potential is negative. At this point, water can flow uphill, down the pressure gradient, from the w ater table up toward the point. (This, in fact, is the source of the well-known capi llary fringe.) The point may not be saturated—in fact, in most alluvial deposits, the point w ill not be saturated—though it likely will be moister than in the absence of the hydraulic lift. Still, the net effect, for this point, is that it went from saturated to unsaturated, whi ch means that less water, not more water, is in the carbon-rich soils. Second, this means that less, not more, N transformations are likely to occur. More importantly, Kellogg et al. (20 08) wasn’t about N transformations at all—this was just a purely speculative paragraph based upon no data that, quite frankly, the editors and reviewers at JAWRA should have asked to be removed. l. 3702-3705: What do you mean by “redoxing agents”? l. 3708-3734: This entire section is poorly referenced. This is nitrogen in riparian and floodplain wetlands, for which there are many studies, and yet only one study is referenced. Granted, the paper is good, and well referenc ed itself, but it seems like you, too, could bolster your argument with additional references , such as the roles played by riparian wetlands in reducing nitrogen loads in agricultura l runoff (Peterjohn and Correll 1984), the roles played by hyporheic flows, including those at t he channel-floodplain interface, in reducing nitrogen in stream waters (Dahm et al., 1998, Hill and Lymburner 1998, Hill et al., 1998), and the role that linked hillslopes-hea dwater wetlands-headwater streams play in reducing nitrogen loads as water flows f rom hillslopes to river networks (Triska et al., 2007).
l. 3835-3836: Add Tockner et al. (2000) to the references here. Junk e t al. (1989) developed the flood-pulse concept for tropical rivers; Tockner et al. (2000) extended the flood-pulse concept to temperate rivers.

Richardson This provides a very good summary of the literature and the conclusions are supported.Responses to Charge Questions

30 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE Snodgrass On lines 233 and 234 the authors suggest that riparian buffer zone s are one of the most

effective tools for mitigating non-point source pollutants. This is true for non-point source pollutants such as nutrients and sediments that might enter riparian areas in groundwater and runoff, but may not be true for other pollutants such as r oad salts and organic compounds. I think we need to be careful of promoting ripa rian areas as a cure for all ills while still clearly indicating where they are useful. Given the length of the document and its focus on downstream effects the author may not need to address this comment in their final edits.

van der Valk Yes. The multiple connections (surface water, groundwater, bi ological) between rivers and

floodplain wetlands were well documented.

Wipfli Yes, to the best of my knowledge, the conclusions are fully suppo rted by the evidence in

the scientific literature. There is strong evidence in t he scientific literature that riparian area wetlands and other waters are physically, biologically, and chemically connected to, and influence, the river network. The evidence reported and ci ted in this review is presented accurately, thoroughly, and clearly.



### b) Does the report include the most relevant peer-reviewed literature on these topics, including evidence of connectivity and isolation? If not please indicate which references are missing.

Reviewer Comments
Cooper See comment 2a) above.
Crumpton See comment 2a) above.

Cummins By and large the report does include the most relevant peer r eviewed literature to address

the question. However I have the following comments and recomm endations. Page Line Comment 7 161 ...rivers. At some point, perhaps here, cases in which headwa ter streams

are not the initial source of river networks should be fla gged. For example, the Yellowstone River (one of the longest and largest un-dammed r ivers in North America) originates from Yellowstone Lake. The lake itself is fed by numerous small tributaries which are not episodic connections . This natural configuration conforms to essentially all human-c onstructed reservoirs in North America. 175 3573 ...outside edges of riparian areas... See comment 26, 559 (Fig. 3-3) . This

implies the width of riparian areas has been defined (as argued at 26, 559, there is little agreement about this, because the width i s dependent upon the function being considered or the management objectives dependent upon the width as define by regulations. For example, fores ters interested in timber harvest will argue for the smallest width po ssible while fisheries managers will argue for a width sufficient to provide re cruitment of LWD.Responses to Charge Questions

31 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE 177 3615 ...such as black willow... As discussed at 74, 1363, the physical bank

stabilization characteristics if black willow need to be balance against the potential disruptive effects on the aquatic ecosystem involved , e.g., stream or wetland. A very important point about connectivity betwee n the riparian zone and the adjacent aquatic system and, therefore, the connec tivity downstream is that the plant species composition of the ripa rian has a very significant impact on the timing and nature of these downstream contributions. (e.g., Cummins et al., 1989). 184 3771-72 Allochthonous inputs...food webs...(reviewed in Tank et al. 2010). Th is

could use some other review references (e.g., Cummins 1974, V annote et al. 1980, Cummins 2002) and many others). [Cummins, K. W. 2002. Riparian-stream linkage paradigm. Verh. Verein. Limnol. 28: 49-58.] 187 3842-44 Thus, lateral... river systems. Here or elsewhere cite Junk et al., 1989. Most stream ecologists would cite this paper as one of the major additions to the River Continuum Concept. [Junk, W. J., P. B. Bayley, and R. E. Sparks. 1989. Th e Flood Pulse

Concept 9n river floodplain systems. Pp 110-127 in : Dodge, D. P. Proceedings of the international large river symposium. Can . Spec. Publ. fih. Aquat. Sci. 106.] 189 3881-82 See also notes about black willow (74, 1363; 177, 3771-72.

Dodds Yes, there is much current and relevant literature cit ed.

La Baugh No response as this is not a focus of my area of exper tise.

Rains See comment 2a) above.

Richardson The literature covered is excellent.

Snodgrass To the best of my knowledge in this area the report does i nclude the most relevant

literature. However, this is not my area of expertise as I have conducted little work in floodplain systems.

van der Valk The relevant literature on floodplains is huge and unequivoca l about the connectivity of

rivers and their floodplains. Although this review does not ci te some relevant literature on floodplain development (e.g., J. S. Bridge. 2003. Rivers and Floodplains: Forms, Processes, and Sedimentary Record . Blackwell), it cites the most relevant reviews on connectivity between rivers and floodplains like Amoros and B ornette (2002). Again, I doubt that the conclusions drawn from the literature reviewe d would be affected in any way because some relevant references were not included. Some relevant papers from outside NA that are missing inclu de:
Boschilia, S.M., E.F. Oliveira, and S.M. Thomaz. 2008. Do aquatic macrophytes co-occur randomly? An analysis of null models in a tropical floodplain. Oecologia 156: 203-214.Responses to Charge Questions

32 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE Henry, C.P., C. Amoros, and N. Roset. 2002. Restoration ecology of riverine wetlands: a 5- year post-operation survey on the Rhone River, France. Ecologica l Engineering 18: 543-554.
Paillex, A., S. Doledec, E. Castella, and S. Merigoux. 2009 . Large river floodplain restoration: predicting species richness and trait responses to the restoration of hydrological connectivity. Journal of Applied Ecology 46: 250-258.
Vervuren, P.J.A., C.W.P.M Blom and H. de Kroon. 2003. Extrem e flooding events on the Rhine and the survival and distribution of riparian plant speci es. Journal of Ecology 91: 135-146.

Wipfli Yes, the report appears to include the most relevant lit erature that shows how off-channel

freshwater habitats are connected to mainstem channels and riverine networks.



### c) Was the reviewed literature cited and summarized correctly? If not ple ase indicate where correction or revision is needed.

Reviewer Comments
Cooper See comment 2a) above.

Crumpton See comment 2a) above.

Cummins Literature was cited and summarized correctly. (Except see note at 184, 3771-72.)

Dodds The only major issue I have with this section is not so clearly separating literature on

riparian areas that are not technically wetlands from those that are. I understand that the authors of this document did not want to leave out ripari an areas completely because it is clear that ANY riparian area is connected to the stream it abuts. However, there needs to be clearer separation of these. Perhaps a specific section on riparian areas generally, then a second on riparian wetland areas. Table 5-2, not only is considering a stream without riparian i nfluence limiting, it will give incorrect results. Also in this table, water storage needs to be mentioned Line 4496, might also want to include work by David Galat:

a. Galat, D.L., Fredrickson, L.H., Humburg, D.D., Bataille , K.J., Bodie, J.R., Dohrenwend, J., Gelwicks, G.T., Havel, J.E., Helmers, D.L., Hooker, J.B., Jones, J.R., Knowlton, M.F., J. Kubisiak, J.M., Mccolpin, A.C., Renken, R.B. & Semlitsch, R.D. (1998) Flooding to restore connectivity of regulated, large-rive r wetlands. Bioscience, 48, 721-733.
b. Galat, D.L. & Lopkin, R. (2000) Restoring ecological integri ty of great rivers: historical hydrographs aid in defining reference conditions for the Missouri River. Hydrobiologia, 422/423, 29-48.Responses to Charge Questions

33 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE c. Galat, D.L. & Zweimüller, I. (2001) Conserving large-river fishes: is the highway analogy an appropriate paradigm? Journal of the North American Benthological Society, 20, 266-279. I am surprised there is not more on the Kissimmee restor ation as wetland connectivity was essential to this project. The Dahm, C.N., Cummins, K.W ., Valett, H.M. & Coleman, R.L. (1995) An ecosystem view of the restoration of the Kissimmee River. Restoration Ecology, 3, 225-238.

La Baugh I am not familiar with all of the literature cited in the document regarding the relation of

open water and wetlands in riparian areas and floodplai ns of streams and rivers to their connection with and influence on downstream rivers, therefor e I am not able to judge whether or not all of the cited literature was summarized correctly.

Rains See comment 2a) above.

Richardson The interpretations of what is known and the limitations of inferences possible from the literature are fine. The authors do a very good job throughout the document of ensuring they point out the uncertainties in demonstrating significant c onnections. Good examples given to describe the types of wetlands and their connections to navigable rivers. I find the use of the term riparian a little confusing. It would be hard to distinguish functionally or structurally in most cases how a floodplai n differed from a riparian area, so to refer to “riparian and floodplain” wetlands seems redunda nt (see definition of riparian on P.26). This also goes to whether there is such a thing as a non-riparian wetland, as a wetland should generate its own riparian area. Perhaps thi s should be defined as a nonfloodplain wetland.

Snodgrass To the best of my knowledge in this area the report does c orrectly interpret and cite the

literature. However, this is not my area of expertise as I have conducted little work in floodplain systems.

van der Valk I am not an expert on riverine hydrology, but I did not find any obvious problems with

literature citations or with the interpretations of the literature.

Wipfli Yes, the literature in this report was cited and summari zed thoroughly and correctly.Responses to Charge Questions

34 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE 

### 3. This report concludes that for non-riparian/non-floodplain wetlan ds that are not connected to the river network through a stream channel (i.e., geographically isolate d wetlands and wetlands that spill into losing streams), connectivity and isolation vary wi thin a watershed and over time, making it difficult to generalize about their connections to, or isolation from, downstream waters. The literature we reviewed does not provide suff icient information to evaluate the degree of connectivity (absolute or relative) of these non- riparian particular wetlands.

a) Are these conclusions supported by the scientific evidence?

Reviewer Comments
Cooper This is correct. Documented evidence of hydrologic connections from non-connected

wetlands to streams is sparse, and the conditions for suc h connection are poorly known. Probably the best large-scale evidence is the long-term data collected in the prairie pothole region by Winter et al., However few such studies occur in the western U.S.

Crumpton The conclusion that in the case of non-riparian/non-floodplain w etlands that are not

connected to the river network through a stream channel, connec tivity and isolation varies within a watershed and over time is well supported by the sci entific evidence.
The conclusion that the literature reviewed does not provide s ufficient information to document the connectivity of these systems is correct, but it should be noted that this is largely because the category includes a mix of wetlands that are truly geographically isolated and wetlands that are clearly connected to downst ream waters. The report should attempt to provide guidance on how to distinguish these two ca tegories (perhaps using soils and other indicators). The report distinguishes geogr aphically isolated wetlands as surrounded by uplands but seems to include in this grouping all non- riparian/nonfloodplain wetlands that do not outlet to a channel. This concept is introduced on lines 52- 54 on page 3 of the Introduction and repeated throughout the report. It is well illustrat ed by Figure 3-18 on page 64 in section 3.4.2. Essentially the report places wetlands that spill over to a “swale” in the category of geographically isolate d wetlands since swales can be “upland”. However, it would also include in this category pr airie pothole depressions that spill over onto wetland flats or slope wetlands rather tha n to a channel. Wetland depressions that spill over to wetland systems (including w etland flats, slope wetlands or hydric swales) should be recognized as a separate category, distinct from wetlands that are completely surrounded by upland and thus more likely to be trul y geographically isolated.

The report provides reasonable coverage of the relevant pee r-reviewed literature on connection and isolation of non-riparian/non-floodplain wetlands to the downstream waters but does fall short in a few areas.Responses to Charge Questions

35 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE The report fails to adequately address the effect of s ubsurface tile drainage on connectivity of these wetlands to downstream waters. The re port recognizes that surface drainage and ditching can directly increase connectivit y to downstream waters (for example lines 5166-5170 on pages 249-250 of section 5.8.3.1). The repo rt states that “When potholes are artificially connected to streams and lakes though drainage, isolation is eliminated and they become important source s of water and chemicals” (lines 4984-4985 on page 242 in section 5.8.1). However, the report is apparently referring only to surface drainage. Little consideration i s given to the importance of subsurface “tile” drainage which is ubiquitous throughout the Co rn Belt and many other areas. The report mentions only briefly that “dra ins fitted at the bottom of potholes connected to shallow subsurface pipes often discharge t o open ditches and streams” (lines 5170-5171 on page 250 of section 5.8.3.1) but is silent on whether this constitutes a direct connection to downstream waters. This is an extremely important issue and the report should clarify the role of subsurface tile drainage (and especially surface intakes to these systems) in providing a connection t o downstream waters. Specifically, do surface intakes of subsurface drainage pipe s (“tile drains”) provide a direct connection to downstream waters for what might otherw ise be considered geographically isolated wetlands?

The report in part uses HGM (hydrogeomorphic) wetland class ification and could benefit from a review of the wetland classes in this syst em. Important HGM classes in the Prairie Pothole Region would include for example depress ions, flats, and slope wetlands. This classification is useful in that it helps to illustrate connections and surface flow paths in these landscapes.
The report should also provide information on the relation ship between soils and wetland classes. Soils can be very useful in determining HG M wetland class, in identifying flow paths and connections, and potentially in di stinguishing geographically isolated wetlands from depressions that are a t least intermittently connected to downstream waters through wetland flats or slo pe wetlands.
The report makes the important point that increased sur face outflow and connectivity is expected in wetter portions of the prairie pothole but ext ends this analysis only as far as the Red River Valley and ignores the much wetter and more interconnected wetlands of the Des Moines Lobe (lines 1434-1437 on page 77 of section 3.4.6 and lines 5138-5143 on page 248 of section5.8.3.1).Responses to Charge Questions

36 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE A broader analysis of this pattern for the Prairie Pothole is provided by Johnson et al. ( 2005. Vulnerability of northern prairie wetlands to clima te change. Bioscience 55: 863-873 ). Their models of wetland water regimes suggest th at spillover to downstream waters is a common occurrence in the wetter portion s of the Prairie Pothole Region. For the Des Moines Lobe, spillover was expected in 87 years over a 95 year weather record. Because of the wetter climate, depressional wetlands on the Des Moines Lobe formed as interconnected systems with significant f low from upslope depressions through wetland flats to downslope depressions and from downslope depressions to receiving streams. In this regard, prairie potholes of the Des Moines Lobe differ from the more isolated basins that are typical of drier parts of the Prairie Pothole region. An analysis of soils illustrates these differences bet ween the more interconnected wetlands of the Des Moines Lobe and the more isolated wetlan ds of the drier portions of the Prairie Pothole Region.
The literature is for the most part cited and summa rized correctly. However, in several places (line 1435-1468 and others), the report inco rrectly describes the subregions of the Prairie Pothole Region, essentially ignoring the De s Moines lobe. This is the southeastern and wettest portion of the Prairie Pothole and as s uggested above, its wetlands might be expected to have greater connectivity to downstream waters.

Cummins The conclusions are supported by the scientific evi dence.

In general they are supported by the literature cit ed. However, I find this section very hard to evaluate objectively because the reason for sepa rating out NRCWs as a class of connectivity is not clear. As noted in the underlin ed portion of the question above, there is no reason for this conceptual category.

There was a lot of discussion at the Committee Meet ing about a reorganization of the information that was presented in the Document. I t hink the general thrust of the recommendation would improve the Document and not require much, if anything, in the way of new information.Responses to Charge Questions

37 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE The organization would not be levels of connectivity but rathe r functional classes of connectivity: hydrologic, physical (geomorphic), chemical (nutrien ts/pollutants), and biological (ecological). Within each of these classes there would be continua of connectivity described as probabilities. Namely spatial and temporal probabilities of degree of connectedness. As was suggested, a conceptual model co uld be presented for each. For example, ephemeral streams have a low probabili ty of connectivity on any given day in any given year, whereas perennial streams have a nea r 100% probability of connectivity along the same time continuum. The more spatiall y separated streams and wetlands of various types are, the lower probability they w ill exhibit high connectivity on any time scale.
This more functional approach would provide, I believe, a be tter frame work for handling the problem of conceptual models for isolated (surrounded by uplands) wetlands and allows for the concept that there are no examples of biologica l isolation, because migrations will always bridge hydrologic, physical, and chemical isolation.

Dodds Yes they are. However, the authors could have made a stronge r statement here. One way to look at the issue is that if a wetland is not connected at all to other waters, then the only output of water must be evaporation. If this is the case the n wetlands must be saline because salts will collect. As many if not most of these wetlands are not highly saline, there is strong indication that most wetlands are indeed c onnected to downstream waters either directly or through groundwater.

La Baugh The overall synthesis of the cited literature provided in t he report supports conclusion 3 in

general. Parts of the text would benefit from revision for c larification and technical accuracy, as noted below.

• Page 15, lines 336 to 344 – What is the source of the definition of “geographically” isolated? Why is it necessary to distinguish between geogr aphical and hydrological isolation? The issue of connectivity would seem to be a fun ction of the movement of water (and as noted on page 49, lines 949 -950 – movement of biota ) independent of “geography.” The reason for the introduction of the concept of geographic isolation is missing. Also missing is a literature citation for the statement that vernal pools and coastal depressional wetlands are incorrectly referred to as geographically isolated. Why does this distinction matter?

• Page 64, Figure 3-18 – An inconsistency appears to exist between what is shown in part B and the definition of “geographical isolation” on page 15, li nes 340 to 342. Why is the non-channelized swale considered to be upland? By the de finition on page 15, the wetland is geographically isolated when completely surro unded by upland. In order for water to exit the wetland to the swale, would not the swale have to be topographically lower than the wetland proper and be adjacent to it? The point raised here simply reinforces the reason for the inclusion of geologi cal isolation in the context of examining connectivity is unclear.

• Page 218, Table 5-3, second entry – Is soil permeability the major factor controlling whether or not a wetland loses water by surface versus grou ndwater? What about theResponses to Charge Questions

38 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE importance of topographic setting with respect to the pre sence of channels or swales (see Figure 3-18B for example)?

• Page 218, Table 5-3, fourth entry - The connection of a non-riparian wetland to other water bodies through groundwater flow involves a time component. Even if the groundwater flow system that hydraulically connects a non-ripa rian wetland with an adjacent surface-water body is simply a local flow syste m, time is a factor related to the influence of the wetland on the adjacent surface-water bod y. If the flow path is one such that a particle of water takes years, decades, or l onger to travel down gradient to the surface-water body, that length of time needs to be con sidered in the determination of how much of an influence the wetland has on the adjacent surface-water body. It might be useful to note that even when the wetlands are c onnected hydraulically through groundwater time affects the influence of the we tland on adjacent water bodies. The subject of length of time of groundwater flow in relation to wetlands is presented in Winter and LaBaugh(2003) cited in the EPA repo rt.

• Page 241, lines 4981 to 4982 – The use of the term impermeable throughout the document can be confusing. In most cases it seems that th e contrast is more likely one of rivers or wetlands in high- permeability terrain in c omparison with those in lowpermeability terrain. In the prairie pothole region some wate r does infiltrate the soil so it would be more precise to indicate the soils and the gla cial till comprise lowpermeability terrain.

• Page 250, line 5175 – One factor that can change the chemical characteristi c of prairie pothole wetlands is loss of sediment due to wind erosion d uring periods when wetlands become completely dry. This phenomenon is documented in LaBaugh e t al., 1996, cited elsewhere in the document. Thus, unaltered wetlands with no surface outlet may also lose nutrients, sediment, and other chemical compou nds during such episodes.

• Page 254, lines 5259 to 5265 – One of the key factors affecting connections between prairie pothole wetlands and streams or river networks is the presence of ditches made by human activity. Mention of this is absent from this fi nding, even though ditching was noted in the supporting text that precedes this section.

• Page 254, lines 5266 to 5269 – Ditching is a key factor enabling sediment, nutrients
, and other chemicals that were present in wetlands to move to streams or rivers. The presence of a ditch to effect such transport is not conve yed in use of the phrase “Hydrologic sink or source functions of potholes can impact m any features...” What exactly is meant by “multiple aspects of flow?” The concer n here is that the finding is imprecise relative to what has been documented in the lit erature. In order for water to move across the land surface to a stream or river, either a surface connection needs to be made by a ditch or wetland water levels must rise to s pill points in their basins that have a natural topographic path to a stream or river. Only when such hydrologic connections are made will water in the wetlands have the capa bility of transporting sediment or chemicals to streams.Responses to Charge Questions

39 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE • Page 256, lines 5311 to 5312 – If the pools lie on impermeable substrates how does water infiltrate to form a shallow flow system? Perh aps the pools lie on lowpermeability substrates rather than impermeable substrate s. Also, if the substrate is impermeable, by definition it will not contain a surfici al aquifer. A low-permeable substrate could contain a shallow groundwater system separa ted from a deeper regional aquifer by a confining bed.



### • Page 270, lines 5617 to 5623 – The content of the paragraph reinforces the need to provide a better definition of “geographically isolated,” as w ell as attribution to the source of that definition earlier in the document

.

Rains SUMMARY

The conclusions are supported by the scientific evidence provided . This is the most difficult task for the authors, because hydrological and ec ological connectivity are not fundamental tenets for these systems. However, I do have com ments regarding some flaws and/or inadequacies in the scientific evidence provided as just ification and regarding the wording of the conclusion, which I think soft-peddles the conc lusion. (See, also, the detailed comments related to the conceptual framework in the section titled “Additional Reviewer Comments” below.)

DETAILED COMMENTS
l. 4004-4017: This is a confusing paragraph. At first, it seems like only depressional wetlands are going to be included, and it’s not until l. 4008 and beyond that other types of wetlands are mentioned. I suggest listing all of the types as a list in the first sentence, then clarifying the details in order thereafter. l. 4025-4098: You might consider wind transported snow as a special case of hydrological connectivity. In that regard, you might consider including Ra ins (2011), who showed that moraine, ice-scour, and dead-ice depressional wetlands ser ve as groundwater recharge focal points because aeolian-transported snow is trapped in the topographic lows in winter and then melts and recharges underlying groundwater immediatel y following breakup in late spring, with the net effect being that groundwater re charge rates in these depressional wetlands is 37%-332% of the broader surrounding landscape. l. 4053-4078: You might also consider discussing the special but very i mportant case of groundwater flow-through wetlands. Groundwater flow-through l akes and depressional wetlands, where surface waters are a surface expression of broader groundwater phenomena, have long been recognized. Born et al. (1979) and Rain s (2011) described groundwater flow-though depressional wetlands in glaciated la ndscapes, Sloan (1972) and Richardson et al. (1992) described groundwater flow-through prai rie potholes in the northern prairie, and Murphy et al. (2008) described groundwat er flow-through depressional wetlands in clay-rich soils with abundant desicc ation cracks and other macropores. Rains et al. (2006) showed that vernal pools in central California are a special case, being groundwater flow-though wetlands supported by a se asonal perched aquifer that is unconnected to the underlying regional aquifers.Responses to Charge Questions

40 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE l. 4100-4116: You might consider explaining why depressional wetlands are so good at storing surface water. Though water can be stored in upl ands, too, surface-water storage in wetlands is more efficient than shallow groundwater stor age in uplands, because wetlands have an effective specific yield of ~1.0 (i.e., the entire empty portion of the basin is available for storage) in most circumstances (Sumner 2007), while upland deposits have a specific yield of ~0.1-0.2 (i.e., only 10-20% of the deposits are voids available for storage) in most circumstances (Johnson 1967). l. 4145-4146: Hammersmark et al. (2008) showed that this dry-seas on baseflow ceased earlier when an incised river was restored to the histo ric floodplain. One of the reasons for this was that evapotranspiration was higher in the restor ed floodplain wetlands than in the previously drier floodplain uplands.
l. 4390-4398: This is the first occurrence of this list, which r ecurs a few times hereafter. In all cases, you should add that wetlands can be connected by gr oundwater connections to one another and to nearby streams. l. 4401-4402, l. 4415-4425: I lump these specific lines together in one com ment to make an important point. In the first case, you state in cl ear, concise, and unequivocal terms that riparian and floodplain wetlands are highly connected to ri ver systems. In the second case, you dither for a few paragraphs, then finally get around to saying that non-riparian and channel origin wetlands might be connected to river syst ems under certain circumstances. You are correct; however, by dithering and then only vaguely suppo rting the idea that nonriparian and channel origin wetlands might be connected to ri ver systems, and then only under certain circumstances, I think that you soft-peddle w hat we know about the flow of water across landscapes. To be honest, all hydrologic syst ems are interconnected to some degree or another—that’s why hydrologists refer to the entir e water cycle environment as the hydrosphere. All we’re really debating here is the degree to which non-riparian and channel origin wetlands are connected to river systems. T here is no bright line between connected and isolated, there is only a vague gray area wher e we might choose to transition from their being a significant nexus to their not be ing a significant nexus. This was a central point to the arguments by Nadeau and Rains (2007), and I think it’s an important argument to make here, because the scientific evidence clearly supports that position. l. 5295-5298: Vernal pools aren’t really located in what most people in the West would consider “coastal areas of the western United States”. For example, Rains et al. (2006, 2008) were working in the Central Valley of California, in ve rnal pools that were 2-3 hours drive from the coast. I think it more correct to jus t say “the western United States” or “Mediterranean-like climates in the western United S tates”. l. 5314-5318: You might consider adding Rains et al. (2006) to the re ferences at the end of this sentence. l. 5385-5387: You might consider adding Rains et al. (2006) to the re ferences at the end of this sentence. l. 5401-5412: There is a key difference between these two types of vernal pools that you have missed. The vernal pools on clay-rich soils are per ched surface-water systems; theResponses to Charge Questions

41 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE vernal pools on hardpan soils are perched surface-water and groundwater systems. This makes them behave very differently from a hydrological perspec tive. Table 5-2, Table 5-3: These tables provide are concise synthesis. Can one be made for rivers?

Richardson The conclusions are supported and carefully reviewed. The connection is supported for some cases, but not for all, so I agree that one cannot c ategorically conclude that this class of wetlands is connected. The role of isolated wetlands i n storing water that may reduce runoff intensity and storm-flow generation to streams is a good idea that deserves further study to empirically back up the simulations presented. Li kewise, the contributions of these isolated wetlands on transformation and storage of n utrients, thereby preventing their transport to rivers could be another important mechanism by which these wetlands contribute to navigable rivers and deserves field trials. The uncertainties associated with the connections of non-floodplain wetlands are carefully acknowl edged for the examples, especially for the example of coastal bays, which have some indications of connections, but not strong, and the authors are careful to address t hat. The prairie potholes likewise occupy a continuum, but most have evidence of some connection. The distinction made to clarify geographic isolation from functional connectivity is useful.

Snodgrass The authors use the indirect argument that headwater stre ams are widespread and high

rates of a number of ecological processes have been mea sured; therefore, these systems must have an impact on downstream rivers. In fact, this i s a general approach that is well founded (lines 450 through 452). However, in places the authors ind icate both pieces of this argument are in place for geographically isolated w etlands—high rates of nutrient removal and extensive coverage of geographically isolated wetla nds—but then only report that the effects of this removal are not reported for downstream waters (see lines 313 through 328). Although conclusion number 4 below begins to addre ss this issue, I think the argument could be made more forcefully. In fact, wh at we know about the effects of impervious surface (only mentioned briefly on line 1360) makes a strong argument for a large impact of wetland loss in any watershed where wetl ands cover a relatively large area—if 25% of a watershed is covered in wetlands and those wetlands are converted to impervious (or less pervious) surfaces then there will be la rge impacts on streams, stream hydrology, geomorphology, ecosystem function, and biological comm unities, ultimately affecting downstream rivers (Paul and Meyer, 2001; Welsh et a l., 2005). The same argument for agricultural systems can be found on lines 1394 t hrough 1400. Given that the depressions that form these wetlands are areas of low or n o surface runoff, a principle we have put to use in our design and management of stormwater runo ff using stormwater management ponds, it is highly likely that loses of geographical ly isolated wetlands have a disproportionally large influence on downstream waters compar ed to upland habitat loss. Therefore, it seems that in many areas (e.g., Atlant ic and Gulf Coastal Plains) the indirect argument for connection and influence of geographically isola ted (but not hydrologically isolated) wetland to downstream streams and rivers is str onger than the authors indicate with this conclusion. See my general post meeting comments for further discussion of this issue.Responses to Charge Questions

42 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE The authors discuss “isolated wetlands that have no hydrologi cal connection to other water bodies” (lines 351 and 352) in a number of places in the manusc ript. I am not aware of a hydrological study of an isolated wetland that has not show n some degree of connection to ground waters (either through recharge or discharge and r echarge). If such studies exist it might be a good idea to give an example and indicate the numbe r of studies that have found no connection. Additionally, lines 1206 through 1209 describe geog raphically isolated wetlands that recharge deep ground water or tha t occur in isolated terminal basins where “evapotranspiration is the only form of water loss. ” I am not familiar with these systems as I work in areas where extensive shallow groundwa ter connections are common. There is no citation with these descriptions either. It woul d be nice to describe how many studies fit these descriptions and if they are limited to desert springs and lake systems such as the Great Salt Lake. Figure 3-18 makes it seem like these systems can be small and similar to geographically isolated wetlands.
Also related to the above comments, in the case study of Caro lina bays the authors suggest that groundwater and surface water connections of bays to st reams are still debated. However, all of the studies to date have documented groundw ater connections and the loss and recolonization of these systems by fishes suggests freque nt surface water connections for bays up to 700 m from intermittent streams (see Snodgrass et al., 1996 and summary argument in Sharitz 2003). Given these considerations it appear s that for Carolina bays at least, connectivity is the norm and isolation rare. On lines 3521 through 3522 the authors indicate that they “consider any evidence of connectivity with a stream to be evidence of connectivity with the river and other downstream waters.” Later (on lines 4097-4098) the authors indicat e wetlands that feed losing streams cannot be considered channel wetlands. Howe ver, in the previous chapter the authors argue that losing streams should be considered connected to more permanently flowing downstream waters.

van der Valk Yes. This category of wetlands, however, contains a mix of wetland types that is so broad and heterogeneous that no definitive conclusions about their hydrologi cal connectivity to rivers could ever be drawn for the entire category. The re are situations where a case for hydrologic connectivity of wetlands in this class to rivers c an be made using soils data, e.g., prairie potholes in Iowa. Although definitive data ar e missing in most cases, it can be inferred that these types of wetlands are connected biologic ally to rivers and vice versa in many, if not all, cases.

Wipfli Question is outside my area of expertise.Responses to Charge Questions

43 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE 

### b) Does the report include the most relevant peer-reviewed literature on these topics, including evidence of connectivity and isolation? If not please indicate which references are missing.

Reviewer Comments
Cooper See comment 3a) above.

Crumpton See comment 3a) above.

Cummins This report includes the most relevant peer-reviewed liter ature on those topics, including

evidence of connectivity and isolation as presented. However, i f a different organization of the report is adopted, as discussed above, a reorganizati on of the references cited would be needed.

Dodds Yes, this is made very clear. Isolation is certainly an issue mostly with the biological data,

and they cover this well.
There has been a good amount of work on groundwater connection s in the Highland Lake District of Wisconsin, and these connections include wetla nds. One reference on this might be Hunt, R.J., Strand, M. & Walker, J.F. (2006) Measuring groundwater-surface water interaction and its effect on wetland stream benthic pro ductivity, Trout Lake watershed, northern Wisconsin, USA. Journal of Hydrology, 320, 370-384.
There is a huge amount of work on hydrologic and chemical connec tion in the Everglades. This should probably be covered a bit better here. Line 4835. Why all of a sudden a section on human alterations here, where there are other human alterations throughout? This section is just a bit i nconsistent with the rest of the report.

La Baugh • Arndt and Richardson discuss hydric soil development in prairie pothole wetlands (Arndt, J.L., and Richardson, J.L., 1988, Hydrology, salinity, and hydr ic soil development in a North Dakota prairie-pothole wetland system. Wetlands, v. 9, p. 93-108) but are not included in the references.

• A useful reference regarding wetland soils and water fl ow in a variety of landscapes is Richardson, J.L., and Vepraskas, M.J., editors, 2001, Wet land soils: genesis, hydrology, landscapes, and classification. Lewis Publishers, Boca R aton, Florida, 417 p.

• Page 283, lines 6053 to 6056 – Entry for the cited literature source is not comple te regarding publication information. The correct, complete entry should be revised as follows –Dickinson, J.E.....2020...Middle San Pedro Watershed, Southea stern Arizona. U.S. Geological Survey Scientific Investigations Report 2010 -5126, 36 p. http://pubs.usgs.gov/sir/2010/5126/

• Page 325, lines 7588 to 7593 – Entries for the cited literature source are not comple te regarding the publication information.Responses to Charge Questions

44 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE The correct entry for the Vining 2002 should be revised as fo llows – Vining, K.C, 2002....Water Years 1981-98. U.S. Geological Survey Water-Resources Investigations Report 02-4113, 28 p. http://nd.water.usgs.gov/pubs/wri/wri024113/
The correct entry for Vining 2004 should be revised as f ollows Vining, K.C., 2004....North Dakota and Minnesota. U.S. Geological Survey Scien tific Investigations Report 2004-5168, 28 p. http://pubs.usgs.gov/sir/2004/5168/

Rains See comment 3a) above.

Richardson The literature reviewed is excellent and represents sta te-of-the-science.

Snodgrass The issues discussed above concerning the importance of is olation for headwater stream

communities also applies to geographically isolated wetlands . As the authors clearly review, isolated wetlands are periodically connected by surface water s to downstream areas that may provide sources of colonist that establish populations in wetland s. These populations can have large effects on wetland communities through predati on, and trade-offs among the competing demands of surviving desiccating conditions and predati on pressures creates adaptations to narrow ranges of hydrological and predator com munity conditions (Wiggins et al., 1980; Wellborn et al., 1996). Therefore, alteration of the isolation or connection of wetlands to downstream communities has the potential to al ter biodiversity associated with isolated wetlands. See Snodgrass et al. (2000) for further dis cussion in relationship to wetland regulations.

van der Valk Yes. It does a good job of reviewing the published literature. However, it is somewhat

ambivalent about the interpretation of some of the litera ture on “clusters” of wetlands. Although wetlands within a cluster evidently are linked, pres umably by groundwater flows, they are considered only linked if there is a surface wate r connection from one wetland in the cluster to a river. The potential for groundwater connection s between isolated wetlands and rivers is never examined. That wetlands like prairie potholes are connected by groundwater flows is well documented. That similar groundwater flows can also connect them to rivers is at least highly probable for some prairie potholes in less h ummocky terrain.

Wipfli Question is outside my area of expertise.



### c) Was the reviewed literature cited and summarized correctly? If not ple ase indicate where correction or revision is needed.

Reviewer Comments
Cooper See comment 3a) above.

Crumpton See comment 3a) above.

Cummins Yes, the literature was cited and summarized correctly

.Responses to Charge Questions

45 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE Dodds Yes, this is cited and summarized correctly.

Line 5177 the word detrimental is loaded, if it is a natura l accumulation, then not quite sure how it is viewed as detrimental.
I am not really clear on how vernal pools are substantially different than the prairie potholes for the purposes of this document. The criteria on 5345 could apply to many of them.

La Baugh • Literature pertaining to the overall topic and prairie pothole wetlands was summarized correctly in general. Areas requiring clarification ar e noted above in 3a.

• I am not familiar with all of the literature cited in the document regarding the relation of oxbow lakes, Carolina and Delmarva Bays, and vernal pools to their connection with and influence on downstream rivers, therefore I am not able to judge whether or not all of the cited literature pertaining to those types of wet lands was summarized correctly.

Rains See comment 3a) above.

Richardson The summary of the literature is very good and the authors ha ve appropriately represented

the collective evidence.

Snodgrass The literature that was reviewed appears to be interprete d correctly and cited appropriately.

van der Valk Yes. However, the use of soil maps, however, to demonstrate ephemeral surface water

linkages between isolated wetlands like prairie potholes and streams is not fully explored. See above. Likewise the possible connection of isolated wetland s to rivers by groundwater flow is largely ignored.

Wipfli Question is outside my area of expertise.Responses to Charge Questions

46 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE 

### 4. This report concludes that while the influence of a particular stream or wetland on downstream waters might be small, the aggregate contribution by an entire c lass of streams or wetlands (e.g., all ephemeral streams in the river network, or a cluster of small wetlands) might be substantial.

a) Is this conclusion supported by the scientific evidence?

Reviewer Comments
Cooper The contribution of streams and wetlands on downstream wate rs is well known for flood water retention (the studies by Novitski 1978 in Wisconsin shoul d be added). Denitrification has been shown in many wetlands. However few other functions have been conclusively demonstrated for many wetland types.

Crumpton The conclusion that in the aggregate, a class of streams or wetlands might have a

substantial effect on downstream waters even though the influe nce of an individual stream or wetland might be small is clearly supported by the scie ntific evidence (and by simple common sense).
The report provides sufficient coverage of the relevant pee r-reviewed literature on this topic although that literature is by design spread througho ut the report in the treatments of streams, riparian/floodplain wetlands, and non-riparian/non-f loodplain wetlands. The literature relevant to this topic was cited and su mmarized appropriately although its dispersion throughout the document makes it less easily acces sible than that of the other topics.

Cummins The conclusions are supported by the scientific evidence.

Dodds Yes, this is a very important point of this document. Th is point is actually true for any nonpoint pollution source, and the entire field of watershed mana gement and TMDL’s is based on this idea. Once the systems are known to be connected to r eceiving waters, then it is a clear fact that small individual systems might have a la rge effect in aggregate.

La Baugh In the section 6 of the document containing the set of conclus ions (pages 266 to 271), the

conclusion noted as 4 above was not presented. Nor was a four th conclusion presented in Executive Summary at the beginning of the report. The absence of a fourth conclusion in the report, accompanied by supporting statements of key findi ngs to support that conclusion, make answering this question and the following qu estions problematic.

Rains SUMMARY

To be honest, I don’t see where you make this case explicitly at all. I do think that it is true, or at least that it can be true. For example, there’s no doubt that obliterating a single headwater stream high up in the watershed will have no measurabl e effect on the large, mainstem river where it discharges to the ocean, but there’ s equally no doubt that obliterating all of the headwater streams in the watershe d will have a measurable andResponses to Charge Questions

47 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE catastrophic effect on the large, mainstem river where it discharges to the ocean. Justice Kennedy, in his opinion in Rapanos v U.S. (2006), would seem to agree. I do think that the basic pieces are in this document to make that case, but I think it important that you explicitly make this case, both throughout the document (e.g ., in a paragraph or section when discussing streams, riparian and floodplain wetlands , and non-riparian and channel origin wetlands) and in a single standalone section, perhaps referencing the voluminous cumulative effects literature (e.g., Bedford and Prest on 1988, Lee and Gosselink 1988, Childers and Gosselink 1990, Johnston 1994, and many others). The latter could be done toward the end of the conceptual model, after you have shown land scape-scale connectivity between all of the disparate pieces separately discussed in t his document. The former could then be done with examples within the individual discussions of the disparate pieces discussed in this document. You already do some of this—for exa mple, you do discuss the role that depressional wetlands play in storing water an d reducing stormflows (l. 4100- 4116)—but you probably should do more and more explicitly state the point that you are trying to make here whenever you do.
There are numerous examples of this with regards to fl ood storage that you could add to those that you already have discussed. Non-floodplain wetland s temporarily store surface water, thereby attenuating and translating flood peaks in downstream river networks (Haan and Johnson 1968, Hubbard and Linder 1986). This phenomenon is so well known that rainfall-runoff models typically have a step when a storm begins where rainfall is abstracted and put into depressional storage and is unavaila ble for runoff throughout the remaining storm (McCuen 2005). However, storage capacity is a finite quantity that can be exceeded, suggesting that flat and depressional wetlands will have the greatest effect during smaller storms (Haan and Johnson 1968). In fact, epheme ral surface-water connections occurring immediately following larger storms are a n indication that storage capacity has been exceeded and subsequent water is immediate ly discharged (Rains et al., 2006, Rains et al., 2008).
There are also implicit examples of both flood storage an d other processes that can be inferred from the literature. Depressional wetlands can focus groundwater recharge. As described elsewhere, Rains (2011) showed this to be the cas e for moraine, ice-scour, and dead-ice depression in southwest Alaska. He did not specific ally upscale—necessary spatial data were lacking—but he did show that these types of wetlands are perhaps the most numerous and conspicuous types of wetlands in these environments, implying that, though the individual effect of one wetland may be negligible, t he cumulative effect of the many thousands of wetlands must necessarily be important. In this case, the effect is implicit, not explicit, but you could nevertheless make this point more strongly by explicitly stating this implicit assumption.

Richardson Given the preponderance of small streams and wetlands that are not navigable in and of

themselves, they in aggregate do contribute enormously to na vigable systems. The conclusions drawn by the authors are sound and well supported by the literature.

Snodgrass Yes the report clearly supports the idea that some wetland s and streams (if not all) make

substantial contributions to the structure and functioning of downstream waters.Responses to Charge Questions

48 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE van der Valk For streams, this conclusion is self-evident and is supporte d by the literature. For isolated

wetland complexes, there are only a few relevant studies . Consequently, although it may be true, it is more of a conjecture than a fact. What exac tly constitutes “a cluster of small wetlands”? How do you draw the boundaries around a cluster? See above.

Wipfli Absolutely yes. This is a key point about headwaters and down stream waterways that

unfortunately can easily be overlooked, and I was pleased t o see this addressed. Individually, small streams do generally not have large infl uences by themselves on downstream processes, but in aggregate they tremendously aff ect riverine networks at the watershed scale.



### b) Does the report include the most relevant peer-reviewed literature on this topic? If not please indicate which references are missing.

Reviewer Comments
Cooper See comment 4a) above.

Crumpton See comment 4a) above.

Cummins This report includes the most relevant peer-reviewed liter ature on those topics, including

evidence of connectivity and isolation. This question has al ready been addressed in detail under the other charge questions. There seems little reason to simply transfer those comments (especially Charge Question 1) to this spot. I fi nd the charge question redundant. Whereas the first three charge questions more or less a pply sections 3, 5 (5.1-5.3) and 5.4 of the report, respectively. There is no separate section that corresponds to Charge Question 4. If one uses the find option in Word and inserts i ntermediate or ephemeral streams or small wetlands in the search, one or both of these appear in essentially every sub-section of the entire report. In reading the report I c oncluded that these entries were accompanied by appropriate citations. The comments provided under Question 3) apply here as well. If the Report was organized functionally, this section would be subsumed under each of the functional conceptual models.

Dodds As far as I know, yes.

La Baugh Insufficient information was provided to enable an answer to the question.

Rains See comment 4a) above.

Richardson The review has covered a comprehensive set of literature r elevant to the topic.

Snodgrass Yes, if the references mention above are included.

van der Valk Yes, the most relevant literature has been reviewed in the report. However, the relevant literature on wetland soils that demonstrates how connected s ome putatively isolatedResponses to Charge Questions

49 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE wetlands like prairie potholes really are is not adequately explored. See Miller et al. (2012) in Wetland Ecology and Management.

Wipfli Yes, the report includes the relevant scientific liter ature on the cumulative effects of

headwaters.



### c) Was the reviewed literature cited and summarized correctly? If not pleas e indicate where correction or revision is needed.

Reviewer Comments
Cooper See comment 4a) above.

Crumpton See comment 4a) above.

Cummins The reviewed literature was cited and summarized cor rectly, or relevant comments were covered under the first three Charge Questions (e.g., comm ents about adaptations by invertebrate life cycles to accommodate periodic drying, in w hich the annual predictable seasonal flows of intermittent streams have more taxa a dapted to the condition than in ephemeral streams, in which annual flows can only be descr ibed in terms of probabilities).

Dodds As far as I know, yes.

La Baugh Insufficient information was provided to enable an answer to the question.

Rains See comment 4a) above.

Richardson The authors have made a very thorough search of the literat ure for appropriate references

and have drawn appropriate conclusions, including pointing out any uncertainties about the conclusions possible.

Snodgrass Yes, again with the consideration of comments included above.

van der Valk Yes. The problem is not with the interpretation of the li terature but with creating an

artificial category of wetlands that contains so many different kinds of wetlands that no general conclusion could ever be drawn for the entire catego ry.
Wipfli Yes, to the best of my knowledge the literature on this top ic was cited and summarized

thoroughly and correctly.51 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE 

## Additional Reviewer CommentsDavid J. Cooper, Ph.D.

53 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE 

### Additional Comments Submitted by Dr. David J. Cooper

Literature Cited
Novitzki, RP. 1978. Hydrologic characteristics of Wisconsin’s wetlands and their influence on floods. Pp. 377-388, in P. Greeson, J. Clark, J.E. Clark (eds). Wetlan d functions and values: the status of our understanding. Proc. National Symposium on Wetlands. Am Wat er Res Assoc, Minneapolis MN.
Thomas C. Winter, Judson W. Harvey, O. Lehn Franke, Willi am M. Alley. 2008. Surface and Ground water, a single Resource. USGS Circular 1139.
Hauer, F. R., Cook, B.J., Gilbert, M. C., Clairain, Jr ., E. C., and Smith R. D.. 2001. The Hydrogeomorphic Approach to Functional Assessment: A Regional Guidebook for A ssessing the Functions of Riverine Floodplain Wetlands in the Northern Rocky Mountains. Speci al Publ. WES, USCOE, Vicksburg, MS. p.255.
Hauer, F. R., Cook, B.J., Gilbert, M. C., Clairain, Jr ., E. C., and Smith R. D. 2000. A regional guidebook: Assessing the functions of intermontane prairie pothole wetl ands in the northern Rocky Mountains. Special Publ. WES, USCOE, Vicksburg, MS. p.189.
THREE papers (PDFs provided) that you might consider refer encing as they present original data on hydrologic connectivity on ephemeral and intermittent streams t o riparian and wetland ecosystems
Shaw, J. and Cooper. D.J. 2008. Watershed and stream rea ch characteristics controlling riparian vegetation in semiarid ephemeral stream networks. Journal of Hydrology 350:68-82.
Westbrook, C., Cooper, D.J., and Baker, B. 2006

. Beaver dams and floods in controlling hydrologic processes of a mountain valley. Water Resources Research 42: W06404, doi:10.1029/2005WR004560
Wurster, F.C., Cooper, D.J., and Sanford. W.E. 2003. St ream/aquifer interactions at Great Sand Dunes National Monument, Colorado: Influences on interdunal wet land disappearance. Journal of Hydrology 271 :77-100.William G. Crumpton, Ph.D.

55 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE 

### Additional Comments Submitted by Dr. William G. Crumpton

My additional comments relate primarily to charge questi ons 3.
Much of our panel’s discussion seemed to focus on issues rela ted to connectivity and while connectivity is important, it is in many ways more important to consi der evidence of influence. This could be especially true in the case of “geographically isolated wetlands”. In fac t, the influence of “geographically isolated” wetlands could be increased by some degree of isolation, for exampl e in the case of sediment retention and flood storage. Isolated depressional wetlands that are connected to downstream waters only during relatively infrequent storm flows could exert substantial influence on sediment transport and storm flows to downstream waters in part due to the relative isolation of these depres sions from those downstream waters. Influence does not require a direct connection and “geographically isolated w etlands” could certainly alter material fluxes to downstream waters. Some of the effects of “geographically isolate wetlands” could be quantified based on available literature as has been done for tributary streams (for example an estimate of the flood storage volume of isolated depressions based on published values of thei r areal extent (for example using the estimates of Miller et al., 2009 for Iowa).
The apparent uncertainty over the connectivity of “geographicall y isolated wetlands” could be greatly reduced and the issues clarified by using an HGM approach to expl icitly considering the links between wetland soils and hydrology. Wetland soils and hydrology are inextricably linked and soils can help in interpreting sources, pathways and frequency of water movement through wetlands and between wetlands and downstream waters. The NRCS technical note on “Soil Hydrodynamic Interpretations of Wetlands” is a very useful resource for this.
The report needs to clearly define and discuss issues rel ated to cropped wetlands. Prior converted cropland and farmed wetlands are two distinct categories of wet land defined by the Food Security Act that have important implications with respect to both wetland pro tection and agricultural production. The 1985 Farm Bill established two categories of cropped wetlands, pri or converted cropland and farmed wetlands.
Prior converted cropland : Wetlands that had been sufficiently drained prior to December 23, 1985 are referred to as prior converted cropland and are not trea ted as wetlands under the Swampbuster provisions of the 1985 Farm Bill. There are no USDA restrictions on fur ther improving or enhancing drainage on prior converted cropland.

Farmed wetlands : Wetlands that had not been sufficiently drained prior to December 23, 1985 are referred to as farmed wetlands and are afforded protection under the Swampbuster provisions of the 1985 Farm Bill. There are restrictions on further improving or enhanc ing drainage on farmed wetlands. Farmers who improve the drainage of a farmed wetland beyond the “scope and effect of the original drainage” could lose all USDA program benefits or face penalties. The se penalties or loss of benefits can cost landowners tens- or even hundreds of thousands of dollars.
The report needs to clearly define and discuss the issues related to subsurface tile drainage and how that influences connectivity of “geographically isolated wetlands ” to downstream waters. In much of the Corn Belt, subsurface tile drainage systems transport most o f the water that leaves agricultural watersheds. ForWilliam G. Crumpton, Ph.D.

56 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE systems with surface intakes, tile drains could provide a direct connection to downstream waters. Regardless of one’s opinion over the importance of this connection, it is un acceptable to ignore this issue in a report that addresses the connectivity and influence of wetlands on down stream waters.Kenneth W. Cummins, Ph.D.

57 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE 

### Additional Comments Submitted by Dr. Kenneth W. Cummins

Additional Comments (via email)
There was a lot of discussion at the meeting about a r eorganization of the information that was presented in the Document. I think the general thrust of th e recommendation would improve the Document and not require much if anything in the way of ne w information.
The organization would not be levels of connectivity but rather functional classes of connectivity: hydrologic, physical (geomorphic), chemical (nutrients/ pollut ants), and biological (ecological). Within each

of these classes there would be continua of connectivit y described as probabilities. Namely spatial and temporal probabilities of degree of con nectedness. For example, ephemeral streams have a low probability of connectivity on any give n day in any given year, whereas perennial streams have a near 100% probability of connectivity along the same time continuum. The more spatially separated streams and wetlands of various types are, the lower probability they will exhibit high connectivity on any time scale.
This more functional approach gives, I believe, a better frame work for handling the problem of conceptual models for isolated (surrounded by uplands) wetlan ds and allows for the concept that there are no examples of biological isolation, because migrations will always bridge hydrologic, physical, and chemical isolation.

Other Additional Comments

Page Line(s) Comments 2 28 ... plants, microorganisms, and... 4 81 replace lack with back 8 176 ...series of complex physical, chemical, and biological alte rations...

10 223 ... lakes and lakes and reservoirs that form nodes in rive r systems. 12 261-2 ...of sediment and organic matter... before they enter... 13 306-8 The impacts ... habitat, and ecology. The concept discusse d in 11, 253-60 also applies

here.

15 334 ...and invertebrates and vertebrates between... (fish and amphibian eggs have been

isolated from migratory ducks feet)

17 398 ... the term... Then why use it? 19 424 ...oxbow lakes, “node” and pater noster lakesKenneth W. Cummins, Ph.D.

58 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE 20 443 ... scientific community... not those ignoring non-peer revie wed literature. Also, the

statement about peer reviewed literature only being used is not true – p 311, 7055, National Research Council 2002 reference was not peer revie wed literature. 21 477-8 Again, I would argue that this report has a more tho rough and unbiased literature review

than most “peer reviewed” papers.
25 539 First Vannote et al., 1980 citation. Introduce River Conti nuum Concept phrase used

therein. 25 546 Fig. 3-2. You need a magnifying glass to distinguish epheme ral streams. 27 583 Use an acronym for riparian/floodplain wetlands (R/FWs) or spell out non-riparian and

channel origin floodplains (NRCWs). Use acronym for both o r spell out both throughout the document.
28 661-2 See comment at 20, 443 above. 33 689-90 ...and references therein). This is a useful phrase to a dd where warranted because it

indicates at least a partial review of the subject is in cluded; could be useful other places in the report. 34 699 ...precipitation and are not seasonally controlled. 34 715 ...Hunter et al., 2005) and have major consequences for the dis tribution and seasonality

of stream biota. 39 774 Fig. 3-10 has a much better representation of ephemeral streams than Fig. 3-2 (25, 546).

42 826 Delete has

. 48 929-31 This is another argument for using link number. (see 24, 531; introduced at 122, 531 as useful but probably should be introduced here.
50 964 Vannote et al., 1980 should also be cited here. 51 1001 ...be eaten by other invertebrates and by aquatic vertebrates , especially juvenile fish that

eventually ...

51 1001 Delete further ; ambiguous. 52 1006 Fig. 3-14. This is an interesting take on the original Va nnote et al., 1980 conceptual

model. Perhaps a citation or two would be warranted here

. 53 1017 ...basin can be transported back to a river only by terrest rial (over land) movement and

not by a hydrological pathway. 54 1047-8 ...100 year floodplain. Introduce the concept of recurrence int ervals (it appears later in

the report. 56 1104 A statement is warranted about the “man-made paving” of essentially all urban

watersheds in the U.S. resulting in quick flow as the rul e.Kenneth W. Cummins, Ph.D.

59 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE 59 1139 The Metolius River emerges and immediately assumes the ec ological characteristics of a

fourth-order river, with no headwater biological inputs and cons tant year around flow and temperature that completely alters life history patte rns typical for streams of the region. (Fig. 3-15E; 57, 1105.) 61 1180 Define stream power (math formula) here or elsewhere. 63 1215 Fig. 3-17. Perhaps point out that C fits the pattern of q uick flow for “paved” urban stream watersheds.
65 1240-42 See comment for 11, 253-60. 66. 162 Fig. 3-19. The use of link number can be seen in the fi gure. The trellis watershed is a

third-order with a link number of 13 and the fourth-order dendritic watershed has a link number of 14. Riparian-dependent headwater ecological effects would be greater in the third order watershed.
73 1344 ...Eikeland 1988, add Rader, 1997, ... [Rader, R. B. 1997. A functional classificat ion of

the drift: traits that influence invertebrate availabilit y to salmonids. Can. J. Fish. Aquat. Sci. 54:1211-1234.] 74 1363 ...movement and alter ecosystem function as in the case i n which stream bank

stabilization is accomplished by planting non-native willow t o replace various species of alder. Alder (nitrogen fixers) litter is utilized at 5 to 10 times the rate of willow in headwater streams. 74 1374 ...al. 2011) and form a discontinuity in the normal stream -order related progression in

stream ecosystem structure and function. (Ward, J. V. and J. A. Stanford (eds.). 1982. The ecology of regulated streams. Plenum, N. Y. 398 p. 81 1151 ...and ephemeral streams, even though these watershed repre sent only ??% (small) of the

land area of the United States. 82 1517-18 Another argument for link number inventory. 82 1519-30 Make it clear that stream order is a geomorphic cl assification and not a blue line map criterion .If the tenets of connectivity in this report ar e to be honored, development of new watershed concepts and advancement in research and land management plans must not be blue line map based. 83 1551-53 As per the statement on 82, 1526 (...Despite this underestimat ion...), this raises

important questions about the data. 85 1604-06 Again, this might be a useful approximation, but it shows t hat, in general, map blue line

analysis cannot be used to clarify the actual physical, che mical, and, especially biological, importance of geomorphic first-order channels in a watershed. 85 1608 ...and river flows, as long as headwater streams are define d as second-order channels.Kenneth W. Cummins, Ph.D.

60 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE 87 1630 ...return interval... First mention of recurrence interval. Here, or elsewhere it should be

defined (calculation method) and its utility discussed. 91 1706 ...Suspended sediment... The question of suspended fine particulate o rganic particles

should be acknowledged. FPOM is a significant contributor to turbidity (first to be entrained on the rising limb of the hydrograph and the last to settle out on the falling limb) and biologically by far the most important component of the suspended load. 93 1763 ...inorganic + organic... First mention of the organic component; should appear earlier. 94 1796 LWD in stream of the western Cascades in Oregon measur ed to have been in place for

over 100 years. 96 1838 ...important habitat for aquatic life... Not just habitat; LWD has a major role as a long

term source of slowly processed DOM and FPOM that is uti lized by stream microbes and invertebrates. 97 1858 ...diel changes typical of intermediate sized streams... a nd rivers. Larger daily

temperature excursions in mid-sized rivers is one of two reasons proposed (Vannote et al., 1980; orders 4-6) for the usually maximized biological diversi ty of these rivers. (Aquatic organisms have differing temperature optima, and a wide daily range of temperature excursion provides more species to spend at le ast part of every 24 hours in their optimum range.) 100 1915 ...chemical linkages through open cycle spiraling. 107 2088 ...terrestrial plant litter... (in addition to leaf litter, other riparian plant par ts can

dominate seasonally, e.g., catkins.)
108 2106 Cite Petersen et al., 1989. [Petersen, R.C., K.W. Cumm ins, and G.M. Ward. 1989.

Microbial and animal processing of detritus in a woodland s tream. Ecol. Monogr. 59:21- 39.
109 2113 In this reference (and Vannote et al., 1980, and most of the other related ones I know of)

headwater streams would be orders 1 – 3.
112 2187 ......downstream (Petersen et al., 1989, Gomi et al., ... 112 2198 ...et al., 2007) or in spring when other plant parts are shed , e.g., bud scales, flowers,

catkins). 113 2219 ...et al., 2005). Diatoms continue to photosynthesize and i nvertebrates continue to feed

and grow at 0 ̊C. In fact, the majority of shredders acco mplish all of their growth in the winter and remain inactive all summer in streams in forested areas (Cummins et al., 1989). 114 2235 The main point of the note here is that it should be a cknowledged that connectivity can

be on a diurnal scale as well as longer time periods. Wee kly grab samples for DOC at 10 locations throughout the Augusta Creek were taken in southw estern Michigan for twoKenneth W. Cummins, Ph.D.

61 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE years. Locations were sampled in sequence each week from 1 through 10 in the same sequential order. The data showed significant differenc es in DOC concentrations between the sites. When samples were taken every 2 hours over 24 hours at 1 site, the difference in the values were equal to the difference in the value s between the 10 sites over 2 years. What appeared to be differences between sites over the 2 yea rs were due entirely to the time of day when the samples were taken which was esse ntially the same each week because of the regular sampling schedule. 119 2374 Many invertebrates have life cycles that “expect” (are adapted to) dry and/or wet and /or

hot or cold periods for the completion of their life cycles. Some may even require these periods. 120 2380 ......drifting insects (Rader 1997, Nakano... 120 2388 ...et al., 2006) and diel invertebrate behavioral patterns t hat are independent of flow

(Rader 1997). 122 2439 ...higher prey and lower predator densities...

129 2605-06 Most often the only shrubs and trees in grassland biomes are along the water courses.

This has significant implications for the in-stream biology (e.g., shading, litter inputs). 135 2737-38 flooding and drying..., spur successional sequences. Flooding is just as important in

forested streams in resetting algal succession. 137 2765 ...surprisingly rapid. Why surprising? This is merely an exam ple of the adaptation one would expect. 138 2808 ...was once limited by floods,... Is there post glacial evidence for this? Or, is “once ”

merely before agriculture cut the prairie? 146 2470 The functional feeding group (FFG) for categorizing fre shwater invertebrates (e.g.,

Cummins and Klug 1979, Merritt et al., 2008) should be used (and defined) throughout the Report. There is a large literature extending over 30 yea rs that utilizes this functional categorization on a world- wide basis (e.g., Cushing et a l., 2002). The FFG meshes well with the concepts of connectivity. Arguably, the best indicator of normal (statistically probable) linkage (coupling) between

riparian vegetation and stream biota is the presence of i nvertebrate shredders (e.g., Cummins and Klug 1979, Grubbs and Cummins 1996, Merritt et al., 2008) . The sequence is well known and has been demonstrated around the world (Cus hing et al., 2006): 1) Riparian leaf is entrained in freshwater system; 2) lea f leaches DOM (up to 40 % of dry mass); 3) leaf rich in carbon, lower in nitrogen, colonized by hyphomeycete fungi (and bacteria), leaf species vary significantly in the length of time required for hyphomycetes to develop hyphal growth in leaf matrix – termed conditioning; 4) shredder invertebrates seek out and feed on leaf or parts of leaf highest in hyphom eycete biomass; 5) shredder feeding produces large amounts of FPOM (< 1 mm particle si ze feces and leaf fragments); 6) shredder feeding and temperature (number o f degree days) accuratelyKenneth W. Cummins, Ph.D.

62 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE predict the period required to process a leaf from a given species of riparian plant (e.g., Petersen and Cummins 1974). [Grubbs, S.A. and K.W. Cummins. 1996. Linkages between ripar ian forest composition

and shredder voltinism. Arch. Hydrobiol. 137:39-58. Merritt. R.W , K.W. Cummins, and M. B. Berg. (eds.). 2008. An introduction to the aquatic in sects of North America (4 th edition). Kendall/Hunt, Dubuque, IA 1158p. . Petersen, R.C. and K.W. Cummins. 1974. Leaf processing in a woodland stream. Freshwat. Biol. 4: 343 -368.] 146 2965 ...richness... Is this species richness? It would be more l ikely density. 146 2966-67 This is a basic tenet of the River Continuum Concept. 147 2977 ...filterers (macroinvertebrates ...suspended FPOM)... Citation? S ee 146, 2970. 148 3016-17 Again, it should be made clear that “richness” is t axa richness. 161 3270 [A note.] This section makes one wonder if the organization of the report should have been by ecoregion, with the four aquatic system types as subheadings under each because the discussion of each of the four is so driven by ecoregion setting. 177 3622 ...length of the riparian area... This is ambiguous? Portion of the stream length that is bordered by riparian vegetation, or should this actually be wid th? 178 3650 ...productivity of vascular plants and algae... 179 3661 stream shading...be beneficial to fish and biota... Cooler temperatures beneficial to (nonfish) biota? According to Q10 relationships, cooler temperat ures would slow production of invertebrates. How would the slowing of production of pote ntial prey for fish be beneficial for fish? 179 3663 ...is used... used by managers? 181 3707 This sentence is too vague. What is being managed? The forest, fish, bank erosion, etc.? 181 3719 This may not be the place to address this, but many ripari an corridors are dominated by

shrubby or tree (red) alders that are nitrogen fixers and constitute a major source of nitrogen.Walter K, Dodds, Ph.D.

63 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE 

### Additional Comments Submitted by Dr. Walter K. Dodds

The meeting confirmed that the document is well written and makes the case for connection to downstream waters for most wetlands and all streams.
In general, I left this meeting with the idea intact that connection of small streams to rivers is important biologically, chemically and physically. Furthermore, in aggregate, many small streams act to define the characteristics of the watershed and influences on the str eams and rivers below. This is true for nutrients (adequately supported in document) and organisms (e.g., Fagan 2002).

The section on streams should include ideas from the liter ature on subsidies and feedbacks. For example marine derived nutrients from spawning salmon can influence small streams, but this material also moves down to larger rivers. There is substantial literature on this idea; the report could start with the book on this issue by Polis et.al. (2004).
Wetlands are clearly connected to downstream waters. Sever al more references could be put in related to this idea (Devito et al., 1999, Richardson et al., 2004, McCormi ck et al., 2006, Strauss et al., 2009). Biological connections can also move nutrients among isolated water bodie s (e.g., Manny et al., 1994, Post et al., 1998).
Some wetlands have very clear and fast connections to downst ream waters, particularly those in more permeable unconsolidated sediments or karst areas (e.g., Malard et al., 1994, White et al., 1995).

Fagan, W.F. (2002) Connectivity, fragmentation, and extinction risk in dendritic metapopulations. Ecology, 83, 3243-3249.
Devito, K.J., Hill, A.R. & Dillon, P. (1999) Episodic sulpha te export from wetlands in acidified headwater catchments: prediction at the landscape scale. Biogeochemistry, 44, 187-203.
Manny, B.A., W. C. Johnson and R. G. Wetzel. (1994) Nutrien t additions by waterfowl to lakes and reservoirs: predicting their effects on productivity and wate r quality. In: Hydrobiologia 279/280:121- 132. (Ed^Eds.
Mccormick, P.V., Shuford, R.B.E. & Chimney, M.J. (2006) Periphyton as a potential phosphorus sink in the Everglades Nutrient Removal Project. Ecological Engineering, 27, 279-289.
Polis, G.A., Power, M.E. & Huxel, G.R. (2004) Food webs at the landscape level, University of Chicago Press. Post, D.M., Taylor, J.P., Kitchell, F.J., Olson, M.H. , Schindler, D.E. & Herwig, B.R. (1998) The role of migratory waterfowl as nutrient vectors in a managed we tland. Conservation Biology, 12, 910-920.
Richardson, W.B., Strauss, E.A., Bartsch, L.A., Monroe , E.M., Cavanaugh, J.C., Vingum, L. & Soballe, D.M. (2004) Denitrification in the Upper Mississippi River: rates, controls, and contribution to nitrate flux. Canadian Journal of Fisheries and Aquatic Sciences, 61, 1102-1112.
Strauss, E.A., Richardson, W.B., Cavanaugh, J.C., Barts ch, L.A., Kreiling, R.M. & Standorf, A.J. (2009) Variability and regulation of denitrification in an Upper Mississippi River backwater.Walter K, Dodds, Ph.D.

64 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE Malard, F., J.-L. Reygrobellet, J. Gibert, R. Chapuis, C. Drogue, T. Winiarsky and Y. Bouvet. (1994) Sensitivity of underground karst ecosystems to human pertur bation - conceptual and methodological framework applied to the experimental site of Terrieu (H erault- France). In: Verh. Internat. Verein. Limnol. 25:1414-1419. (Ed^Eds.)

White, W.B., D. C. Culver, J. S. Herman, T. C. Kane and J. E. Mylroie. (1995) Karst Lands. In: Am. Sci. 83:451-459. (Ed^Eds.)James W. La Baugh, Ph.D.

65 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE 

### Additional Comments Submitted by James W. La Baugh

Post meeting comments

In Reference to Charge Question Number 3, I offer the f ollowing text as one possible solution to the dilemma posed by use of the term non-riparian and channel origin wetl ands.
EPA connectivity panel - wetland classification note and sugges tion
One document that discusses various aspects of wetlands in relation to hydrological characteristics is
Winter, T.C., and Woo, M-K. 1990. Hydrology of lakes and we tlands, p. 159-187, in Wolman, M.G., and Riggs, H.C., (eds.) Surface Water Hydrology. The Geology of North America, volume O-1. Geological Society of America, Boulder, Colorado.
In this document the authors note that existing classifica tions are not easily unified. In Winter and Woo (1990), a variety of lakes and wetlands were examined in the c ontext of geologic settings, hydrologic processes controlling water balances, and physiographic sett ings.
In the EPA connectivity draft, the need to define channel or igin wetlands is not compelling. If channel origin wetlands were simply thought of in terms of being the headwate rs of a river, the need to include them as a separate category is eliminated. They would fall into the category of being associated with a river. The resul t would be two classes of wetlands, those associated dire ctly with rivers, riverine wetlands (borrowing from Winter and Woo) - river headwater, riparian, and floodplain wetlands ? and those not directly associated with rivers, non-riverine wetlands. Use of these two simple te rms, riverine and non-riverine wetlands, also makes a distinction among wetlands: the first, those wetlands mor e likely to be directly connected by a surface water connection with a river, and second, those wetlands less li kely or unlikely to be directly connected by a surface water connection with a river. I suggest you substitute river headwater wetlands for channel origin wetlands in the text and include them in text pertaining to riparian and floodplain wetlands. Then substitute non-riverine wetlands for non-riparian wetlands throughout the doc ument. Such revision might solve the wetlands classification dilemma discussed on January 30, 2012 d uring the panel meeting.
As an aside, Plate 2 from Winter and Woo (1990) is a nice p ortrayal of the fact that about half of North America is not humid. A figure for the lower 48 states de rived from that plate is Figure 14, page 21 in
Reilly, T.E., Dennehy, K.F., Alley, W.M., and Cunningham, W .L., 2008. Ground-Water Availability in the United States. U.S. Geological Survey Circular 1323, 70 p. http://pubs.usgs.gov/circ/1323/
although the figure in Reilly et al. (2008) does not feature the gradients within the semi-arid to arid region shown in the plate of Winter and Woo (1990).
Comment on organization of the document: It would be useful to consider reorganization of the docum ent. Conceptual framework material regarding connectivity and influence appearing in both the stream (sec tion 4) and wetlands (section 5) sections could beJames W. La Baugh, Ph.D.

66 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE moved to section 3 (A conceptual framework) for consistency and clarity of presentation. Readers could then be referred to aspects of this common framework as needed in subsequent discussion of the relation of streams and wetlands to rivers.
One way of organizing a synthesis document is to present the conceptual framework as the main body of the text, with examples from different settings shown as ‘boxe s’ or ‘sidebars’ – see Winter et al. (1998) as an example - http://pubs.usgs.gov/circ/circ1139/ [this reference is cited in the current version of the document]. Another way of organizing a synthesis document is to presen t the conceptual framework as the main text, using ‘boxes’ interspersed to highlight particular technical nuances, with case studies as part of the text appearing after presentation of the conceptual framework – see Healy et al. (2007) as an example - http://pubs.usgs.gov/circ/2007/1308/

Comment regarding the definition of groundwater in the glossar y: The definition is correct. One of the other reviewers suggest ed labeling all subsurface as groundwater. Water in the unsaturated zone is not groundwater. See also page 4 of Heath, R.C., 1983, Basic ground-water hydrology U.S. Geological Survey Water Supply Paper 2220, 84 p. http://pubs.usgs.gov/wsp/wsp2220/

Comment regarding use of the term watershed: The document never clearly states that the term watershe d as used in the report refers to surface water watersheds. It would be useful to note this convention when the word is first used. I may have missed something, but did not find groundwater watersheds mentioned in the text. Somewhere in the introduction, readers would benefit from a brief statement that groundwa ter watersheds also exist but might not coincide with surface water watersheds. Furthermore the boundaries of those watersheds can change over time in response to changing hydrologic conditions. This subject may fit in when the concept of groundwater flow systems is introduced. As noted in my first comment rega rding question 1. Figure 3-5 is inaccurate in its portrayal of local, intermediate, and regional flow syst ems. It would be better to use Toth’s figure to do that . A local flow system is one in which groundwater flows from a water table high to an adjacent lowland. An intermediate flow system is one in which groundwater flows from a water table high to a lowland that is not immediately adjacent to the water table high. If the depth to width ratio of the aquifer is large enough, a regional flow system may also be present. Topographic divi des do not always coincide with water table highs. Variability in the presence or absence of coincidence of surface water and groundwater watersheds is documented in Winter, T.C., Rosenberry, D.O., and LaB augh, J.W., 2003, Where does the ground water in small watersheds come from? Ground Water, volume 47, number 7, pages 989-1000.

Comment about illustration of hydrologic landscapes of the conti nental United States and Alaska and Hawaii: Mention was made during the discussion that it might be use ful to provide readers with the spatial context of ecoregions and hydrologic landscapes. Figure 8 on page S79 of Woll ock et al., 2004 cited in the EPA document is the one that was suggested. It is also possible that inclusion of this figure, as well as the text needed to explain the content of the figure, might distract fr om the main focus of the conceptual framework because of the detail involved.James W. La Baugh, Ph.D.

67 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE Comment about illustrating effects of pumping on groundwater f low paths interacting with a stream: Figure C-1 on page 15 of Winter et al. (1998) shows effect of a pumping well on changes in groundwater flow paths.

Note about example illustrations Sources of hydrologic processes or connections (flow path) illus trations are provided herein. These are provided simply as examples of ways flow processes or connec tions have been illustrated in a variety of settings apart from the more general diagrams used from the W inter et al. (1998) reference in the EPA connectivity document.
[Note: the following two references are key citations for Florida wetlands that were not included in the EPA document, but should be. Essential references]

[Essential reference ] Haag, K.H., and Lee, T.M., 2010, Hydrology and ecology of fr eshwater wetlands in central Florida – A primer. U.S. Geological Survey Circula r 1342, 138 p. http://pubs.usgs.gov/circ/1342 [Figure B-1, page 17 – flow in relation to seepage wetlands; Figure 5, page 21 – flow in Florida karst terrane]

[Essential reference ] Lee, T.M., Haag, K.H., Metz, P.A., and Sacks, L. A., 2009, Comparative Hydrology, Water Quality, and Ecology of Selected Natural and Augme nted Freshwater Wetlands in West-Central Florida. U.S. Geological Survey Professional Paper 1758, 152 p. http://pubs.usgs.gov/pp/1758/ [Figure 1, page 4 – water budget of isolated wetland with fluc tuating water level; Figure 11, page 24 – example of flow system in relation to wetland]
Buszka,P.M., Cohen, D.A., Lampe,D.C., and Pavlovic, N.B ., 2011, Relation of Hydrologic Processes to Groundwater and Surface-Water Levels and Flow Directions in a Dune-Beach Complex at Indiana Dunes National Lakeshore and Beverly Shores, Indiana. U.S. Geologi cal Survey Scientific Investigations Report 2011-5073, 75 p. http://pubs.usgs.gov/sir/2011/5073/ [Figure 3, page 5 – Effect of tile drain on flow]

[Essential reference ] Tribble, Gordon, 2008, Ground Water on Tropical Pacific Island s—Understanding a Vital Resource. U.S. Geological Survey Circular 1312, 35 p. http://pubs.usgs.gov/circ/1312 [Page 4 – Figure showing surface and groundwater flow paths; P ages 10 and 11 - various groundwater flow settings ]
Faunt, C. C., editor, 2009, Groundwater availability of the C entral Valley Aquifer, California. U.S. Geological Survey Professional Paper 1766, 225 p. http://pubs.usgs.gov/pp/1766 [Figure A9, upper part, page 21 – surface and groundwater flow paths in the Sacramento Valley]James W. La Baugh, Ph.D.

68 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE Barlow, P.M., 2003, Ground Water in Freshwater-Saltwater Environments of the Atlantic coast. U.S. Geological Survey Circular 1262, 113 p. http://pubs.usgs.gov/circ/2003/circ1262/ [Figure 3, page 4 – Surface water and groundwater flow paths in the Atlantic coastal plain]
Izbicki, J.A., Johnson,R.U., Kulongoski, J., and Predmore, S., 2007, Ground-Water Recharge from Small Intermittent Streams in the Western Mojave Desert, Ca lifornia. Chapter G in Stonestrom, D.A., Constantz, J.
, Ferré,T.P.A. and Leake, S.A., editors, 2007, Ground-Water R echarge in the Arid and Semiarid Southwestern United States. U.S. Geological Survey Professional Paper 1703 http://pubs.usgs.gov/pp/pp1703/ The entire report is a large document so chapter link i s provided below. http://pubs.usgs.gov/pp/pp1703/g/ pp1703g.pdf [Figure 4, page 163 – hydrologic features of intermittent stre ams in the Mojave Desert]

Planert, M., and Williams, J.S., 1995, Ground Water Atla s of the United States - California, Nevada. U.S.Geological Survey Hydrological Atlas 730-B, http://pubs.usgs.gov/ha/ha730/ch_b/gif/b025.gif (Also available as an Adobe Illustrator eps file) [Figure 25 – block diagram of basin types showing groundwater flow relations to types of playas]

* Documents referred to in general discussion, but not cri tical for the EPA document, except where noted :

Document related to the fact the concept of average conditions is outdated: Milly, P C. , J Betancourt, M Falkenmark, R M Hirsch, Z W Kundzewicz , D Lettenmaier, and Ronald J Stouffer , 2008: Stationarity is dead: Whither water management? Science
, 319(5863) , 573-574.

Document related to conceptual framework of geomorphology in relation to milldam: Merritts, Dorothy, Rahnis, Michael, Walter, Robert, H artranft, Jeff, Cox, Scott, Scheid, Chris*, Potter, N oel*, Jenschke, Matthew*, Reed, Austin*, Matuszewski, Derek*, K ratz, Laura*, Manion, Lauren*, Shilling, Andrea*, Datin, Katherine*, 2011 (in press), The rise and fall of Mid-Atlantic streams: Millpond sedimentation, milldam breaching, channel incision, and stre am bank erosion: Reviews in Engineering Geology, special issue on “The Challenges of Dam Removal an d River Restorations”, editors Jerome V. DeGraff and James E. Evans.

Document related to hydrological and biological interrelations pertaining to removal of

invasive species from riparian zones:

Shafroth, P.B., Brown, C. A., and Merritt, D.M., edi tors, 2009, Saltcedar and Russian Olive Control Demonstration Act Science Assessment. U.S. Geological Su rvey Scientific Investigations Report, 2009-5247, 143 p. http://pubs.usgs.gov/sir/2009/5247/James W. La Baugh, Ph.D.

69 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE Document pertaining to analysis of changing hydrologic condition s in relation to potential for Devils Lake to spill to a river:
Vecchia, A.V., 2008, Climate simulation and flood risk analys is for 2008-40 for Devils Lake, North Dakota: U.S. Geological Survey Scientific Investigations Report 2008-501 1, 28 p. http://pubs.er.usgs.gov/usgspubs/ sir/sir20085011

.

Document that discusses the relation of hydraulic conductivity to presence/absence of groundwater watershed divides:

Winter and LaBaugh (2003) cited in the EPA document. The so urce of the information regarding the importance of moderate to highly permeable versus poorly per meable geologic substrates is Haitjema, H.M., 1995. Analytic element modeling of groundwater flow. Academic P ress, San Diego, California.

Documents pertaining to overviews of wetlands in the Nebraska Sandhills:

[Essential reference] Novacek, J.M., 1989, The water and wetland resources of the Nebraska Sandhills, in van der Valk, A., ed. Northern Prairie Wetlands, Iowa S tate University Press, Ames, Iowa, p. 340-384.
Gosselin, D.C., 1997, Major-ion chemistry of compositional ly diverse lakes, Western Nebraska. U.S.A.: implications for paleoclimatic interpretations, Journal of Paleolimnology, 17:33-49.

Document related to presence and characterization of pl ayas:

[Essential reference] Wood, W.W., 2002, Role of ground wat er in geomorphology, geology, and paleoclimate of the southern High Plains, USA: Ground Water, v. 40, p. 438-447.

Document providing details about the dynamic nature of hydrologica l and biological interactions of prairie wetlands:

Winter, T.C., ed., 2003, Hydrological, chemical, and biologi cal characteristics of a prairie pothole wetland complex under highly variable climate conditions – The Cottonwood L ake area, east-central North Dakota: U.S. Geological Survey Professional Paper 1675, 109 p. http://pubs.usgs.gov/pp/1675/ report.pdf

Document related to movement of nutrient plume from infiltr ation ponds to nearby lake:

McCobb et al., 2003, Phosphorus in a Ground-Water Contaminant Plume Dischargi ng to Ashumet Pond, Cape Cod, Massachusetts, 1999. U.S. Geological Survey Wat er-Resources Investigations Report 02-4306, 69 p. http://pubs.usgs.gov/wri/wri024306/James W. La Baugh, Ph.D.

70 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE Document related to irrigation canal recharge of groun dwater as source of baseflow in rivers inhabited by endangered fish species:
Ely, D.M., 2003, Precipitation-Runoff Simulations of Curre nt and Natural Streamflow Conditions in the Methow River Basin, Washington. U.S. Geological Survey Water -Resources Investigations Report 03-4246, 43 p. http://pubs.usgs.gov/wri/wri034246/Mark C. Rains, Ph.D.

71 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE 

### Additional Comments Submitted by Dr. Mark C. Rains

REVIEWER COMMENTS ON CONCEPTUAL FRAMEWORK:

SUMMARY
The key flaw in the document is that you arbitrarily brea k the landscape into three components, make the focus of the document on the individual discussions of those thre e components, and therefore make it difficult for you to show the inherent connectivity across these component s. To counter this, I think that you should make the conceptual framework the highest order of organization in this document. The conceptual framework should be the central point of the document—the re st of the document should be to support and better explain this conceptual framework. Then conceptual f ramework should start with the premise that all components of the landscape are connected, and that what di ffers is the degree to which they are connected and the importance of those connections to downstream syste ms. You should clearly explain hydrological, chemical, and biological connectivity—but especially hydrological connectivity—in the context of the relevant literature (e.g., Pringle 2001, Pringle 2003a, Pringle 2003b, Freeman et al., 2007), using clear diagrams to illustrate that connectivity extends from ridges to reefs and connects all of the individual elements discussed in the document. You also should clearly explain the broader conceptual framework that you build relating to the five functions or roles that wetlands and streams play (e.g., source, sink, etc.). Last, you shoul d explain how this landscape-scale connectivity means that the cumulative effects of many wetlands and streams can be large, even if the individual effect of one w etland or stream may be small. This, then, should the foundation to which you return throughout the document, alwa ys reminding the reader about how the supporting information in each of the three individual componen ts relates to this conceptual model, and showing specifically how connections and their downstream effec ts are clear in some cases and not so much in others.

DETAILED COMMENTS General Comment: Throughout the document, there were terminol ogy problems that make the basic conceptual framework and the scientific evidence difficult to follow. The first problem relates to the various uses of the terms headwaters, headwater streams, and stre ams. These are often used interchangeably, even though they are not commonly used interchangeably, and are not def ined as such in the Glossary. To improve clarity, the standard definitions in the Glossary should be used throughout the text. The second problem relates to the use of connectivity. At times, it is used i ndependently; at other times, it used following a specific modifier (e.g., biological connectivity). This would not be a problem if independent usage implied any or all kinds of connectivity. However, that doesn’t seem to be t he case; rather, independent usage often seems to imply hydrological connectivity, and perhaps even surface-wate r connectivity (e.g., l. 594-597). To improve clarity, independent usage should refer to the existence of any kind of connectivity, while modified usage should refer to the existence of a specific kind of connectiv ity.
General Comment: There are significant problems with some o f the technical aspects of the conceptual framework, particularly in relation to how water gets from uplands to wetlands or streams or between wetlands and streams. This is a critical part of the conc eptual model, because it underlies the complexMark C. Rains, Ph.D.

72 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE pathways and controls on hydrological connectivity. Lacking a prope r conceptual framework in this regard, the document will fail to make a strong case not only for h ydrological connectivity but also for all types of connectivity at spatial and temporal scales that matter in a regulatory environment. I make numerous specific comments in relation to this below.
l. 522-523: Rains et al. (2006, 2008) would be good references for this condition.

l. 534-536: This sentence concludes that water flows “downhill”. This isn’t actually true. Water flows downgradient, where gradient is primarily due to differe nces in elevation (i.e., the downhill part of downgradient) and pressure. Pressure plays important roles i n surface-water flows, but plays even more important roles in groundwater flows, including groundwa ter flows as they relate to the conceptual framework and the scientific evidence presented throughout each of the subsequent chapters.

l. 575-577: This is not the correct federal definition of a we tland. The federal definition of a wetland is a regulation—which carries the full force of law—that can be found at 33 CFR 328.3(b): “The term ‘wetlands’ means those areas that are inundated or saturated by surf ace or ground water at a frequency and duration sufficient to support, and that under normal circumstances do support, a prevalence of vegetation typically adapted for life in saturated soil conditions. Wetlands gener ally include swamps, marshes, bogs, and similar areas.” This is very similar to a definition used late r in the document (l. 3455-3456). What the authors refer to here is the Corps of Engineers Wetlands Delineation Manual (U SACE 1987), which is guidance—which does not carry the full force of the law—on how to delineate a we tland and not a regulation—which does carry the full force of the law—on how a wetland is defined. One benefi t of using the correct federal definition of a wetland found at 33 CFR 328.3(b)—which is more generic and incl usive, with rather vague boundaries—is that you won’t struggle so much in trying to explain what yo u are considering a wetland in the riparian and floodplain wetland discussion (l. 3531-3540).
l. 613-614: There are two primary types of aquifers: unconfined and confined. In unconfined aquifers, the upper surface of the saturated zone is defined by the water table ; in confined aquifers, the upper surface of the saturated zone is defined by the confining layer, and the w ater in the saturated zone is under pressure and will rise up to the potentiometric surface if the confining layer i s perforated (e.g., by a piezometer or even by a natural fracture, as occurs at many springs). See my comm ent titled “Figure 3-4”, below.
l. 614-615: This is an inadequate definition of groundwater, bec ause it leaves the issue of water in the unsaturated zone undefined. I suggest that you define groundwater as all water underground, be it in the unsaturated or saturated zones, then distinguish between the two when necessary by referring to them specifically as unsaturated-zone (or vadose-zone) groundwate r and saturated-zone groundwater, respectively.
l. 615-616: There are many saturated deposits that we do not c ommonly call aquifers. Clays, for example, are commonly saturated but are not commonly called aquifers, and are instead commonly called aquitards, perching layers, or confining layers, depending upon the role they are playing. Perhaps you mean highly permeable instead of just permeable, but if so then you chose poor examples as soil could be anything, including low-permeability clay-rich soils, and rock h as extremely low primary permeability, though it can have relatively high secondary permeability if there are abund ant and well-connected fractures. You might instead say: “Relatively highly permeable materials (e. g., sand and gravel) that are saturated and in which groundwater is stored and transmitted are referred to as aquifers.”Mark C. Rains, Ph.D.

73 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE Figure 3-4: This is an oversimplification that affects your conceptual framework. I suggest that you show both unconfined and confined aquifers here. I know that this is a bit confusing, but is critically important in understanding connectivity. Many waters are hydrologically connecte d by unconfined aquifers, but many others are hydrologically connected by confined aquifers, espe cially where confined aquifers are perforated and regional groundwater discharges to streams and rivers (e.g., Kish et al., 2010) or surface water recharges regional groundwater (e.g., Sinclair 1977).
l. 628-630: Kish et al. (2010) would a good reference at the end of the last clause as they showed that the vast majority of flow in the Hillsborough River, west-central Florida, was groundwater discharged from the Floridan aquifer, primarily at a single spring.
l. 631-648, Figure 3-5: I’ve lumped the text and figure here, becaus e they are so closely related.
There are quite a few things wrong here, which stem from a n oversimplification on the part of Winter et al. (1998), which is the referenced paper but not the original work, and a misinterpretation on the part of these authors. The original work, cited in Winter et al. ( 1998), was by Toth (1963). Haitjema and Mitchell-Bruker (2005)—who, incidentally, were students of Toth’s—showed that Tot h (1963) was correct, but only for certain cases such as the special case in which he was working. The truth is somewhat more complicated, and relates to important controls by climate and geology, especially geol ogic heterogeneity. Still, you might decide to keep this, subject to some comments below, because there’s no thing really wrong with using terms like local and regional groundwater flows. (Although I must admit that I ’ve never understood the distinction between intermediate and regional groundwater flows.) If you do, howeve r, you need to revise Figure 3-5, which is incorrect. Local groundwater flows are from a local high to a local low. This is the case in Figure 3-5. However, intermediate and regional groundwater flows are la rger in spatial scale and cross one or more groundwater divides (i.e., they cross under one or more poten tial local groundwater flows). This is not the case in Figure 3-5; the intermediate groundwater flow is fr om a local high to a local low (i.e., it’s another local groundwater flow) while the origin of the regional groundw ater flow is a bit unclear.
Regardless, I think that this is an incomplete conceptua l model of flow from uplands to rivers and wetlands. There actually are four pathways that water can take f rom an upland to a river or wetland (Figure 1; Knighton 1998).

• Saturated Groundwater Flow (Pathway 1 in Figure 1): This i s common flow of groundwater through the saturated zone. In this case, this would be an example of a local groundwater flow, though in other cases these might be intermediate or regional groundwater flows.

• Throughflow (Pathway 2 in Figure 1): This is quick flow thr ough the unsaturated zone. This is commonly rapid flow through preferential flow paths, which can be so il cracks, animal burrows, or naturally formed soil pipes.

• Infiltration-Excess Overland Flow, or Hortonian Overland Fl ow (Pathway 3 in Figure 1): This is overland flow where there is an unsaturated zone between the overland flow and the water table. This occurs when the rainfall rate exceeds the infiltration rate, a thi n layer of saturation blankets the surface, and excess rainfall runs off.Mark C. Rains, Ph.D.

74 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE • Saturated Overland Flow, or Dunne’s Mechanism of Overland F low (Pathway 4 in Figure 1): This is overland flow where the water table has risen to the surface and subsurface storage is full. This area varies through the course of the year and a given storm, giving rise to the term variable source area.
This is a more complete and technically correct conceptua l model on which to base your reasoning. This is particularly true, because this emphasizes an important poi nt, which I don’t think comes through in the document, which is that headwaters continue from the headwat er stream up to the summit of the adjacent hillslope. Headwater streams and adjacent hillslopes a re, in fact, integrally connected, to the extent that headwater streams cannot exist absent the adjacent hillslop es. This point is central to the argument made by Nadeau and Rains (2007), and can be seen (explicitly, in som e cases) in the way that they discuss the references therein. (See, specifically, the way they dis cuss Triska et al., [2007] and Meyer et al., [2007], though both are referred to not as “2007” but, rather, as “ this issue”.)
l. 676-679: Your definition of alluvium is somewhat confusing, in t hat there is a separate item in the list that comprises “at the base of a mountain”, which could be eit her an alluvial fan (i.e., a fan of deposits deposited by water flowing off of a hillslope and into a valley) or a colluvial fan (i.e., a fan of deposits deposited by gravity pulling dry materials down a steep hillslope).

Figure 1. This is copied from Knighton (1998). The text a bove refers to this figure.

l. 720-722: You might follow this with a specific example. For exa mple, wetlands can be seasonally isolated, connected by groundwater flows, and connected by surface-water a nd groundwater flows (Rains et al., 2006, 2008).Mark C. Rains, Ph.D.

75 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE l. 794-796: A good reference for the first three items in thi s list would be Hammersmark et al. (2008); a good reference for the fourth and last item on this list would be Wolman and Miller (1960).
l. 896-899: A stream or wetland also can provide different fu nctions at the same time, depending upon perspective. Rains et al. (2006) showed evidence that vernal pools simultaneously serve as a sink for nitrogen and a source for organic carbon, because nitrogen-rich/orga nic carbon-poor groundwater flows into vernal pools, the nitrogen is uptaken and converted to organic carbon, and nitrogen-poor and organic carbon-rich surface water and groundwater flow out of the vernal pools.
l. 990-993: The parenthetical list of “internal components” inc ludes “alluvium” and “geologic materials”, but alluvium is a geologic material. I suggest omitting “geologi c materials”.
l. 1016-1018: Water-borne contaminants can still be transported from a closed-basin depression to a river through groundwater flow.
l. 1053-1055: Rains et al. (2006, 2008) would be good references for t his condition.
l. 1056-1059: You might also mention that downstream transport of seeds and/or propagules and seasonal flooding of riparian/floodplain wetlands is essential fo r the recruitment of vegetation, especially willows and cottonwoods (McBride and Strahan 1984, Scott et al., 1996, Ma honey and Rood 1998).
l. 1079-1222: I think that this entire discussion could be improved if it were integrated to include both climate and watershed characteristics at the same time, using Winter (2001) and Wolock et al. (2004) as the basis for the discussion. This is especially apparent when you compare t he different the different hydrographs, which you try to do only in the context of climate, but are, in fa ct, the result of climate operating on watershed characteristics, an inconvenient fact that you end up having to mention briefly in l. 1134-1135.
l. 1080-1081: I don’t think that this statement is technically t rue, given the importance of geology, topography, and land cover. It’s probably better to say that “Climate determines the amount, timing, and duration of water available to the watershed.”
l. 1092-1093: How are you defining water surplus? Is it precipitat ion minus evapotranspiration? If so, then this sentence isn’t always true because the highest water surplus in snowy catchments is in mid-winter, when snowfall is greatest and evapotranspiration is negligible, bu t flow is low because most of the water is locked up in the snowpack storage.
l. 1098-1104: The first clause in the first sentence is only half true. See the descriptions of the two types of overland flow in my comment titled “l. 631-648, Figure 3-5” above. B ecause you start with only a half true premise, your subsequent examples are not altogether true. For example, overland flows can occur simply where water tables are shallow, regardless of rainfall intensities.
l. 1194-1200, Figure 3-17: I’ve lumped the text and figure here, becaus e they are so closely related. The paragraph uses incorrect terminology. See my comment titled “l. 615-616” above. There isn’t such a thing as an “impermeable aquifer”, because an aquifer must be able to store and transmit water, by definition, and a deposit that is impermeable cannot do either, also by defi nition. Similarly, all aquifers are permeable, so theMark C. Rains, Ph.D.

76 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE term “permeable aquifer” is redundant. Also, permeabilit y is just one part of what controls the direction and rate of groundwater flow. Hydraulic head is the other part. Therefore, the entire discussion here about how permeability controls the direction of groundwater flow is no t entirely correct. However, the general themes in the paragraph and in the figure are not entirely inco rrect, except for the incorrect terminology in both the paragraph and the figure legend and explanation. Therefore, I think this can all be rescued, if the terminology is corrected and the controls on the direction and rate of groundwater flow are better explained. This can all be done better if you adopt the more complete and technically c orrect conceptual model I suggest in my comment titled “l. 631-648, Figure 3-5”.

l. 1223-1318: This is a bit of awkward section because distribution is equally controlled by climate and geology, so this isn’t really a standalone factor equal in importance to climate and watershed characteristics. You should probably state as much at the start, and could readily reference Tihansky (1999) as an example, as she shows that climate and geology control the distribution of s inkhole depressions in Florida, most of which are wetlands or lakes, particularly concentrating them in west-central Florida.
l. 1274-1278: This is not exactly true. Floodplains typically don’t flood uniformly laterally away from the channel; rather, floodplains typically flood by engaging sec ondary and other paleochannels, sometimes by groundwater upwelling, other times by overbank flow (Tockner et al., 2000). These secondary and other paleochannels are all over the floodplain, and can be at the e xtreme edge of the floodplain complex, and the effect is that riparian/floodplain wetlands do not connect s trictly as a function of distance from the main channel.
l. 1408-1413: Another excellent example is Hammersmark et al. (2008) , who showed that the restoration of rivers, where incised channels are backfilled and the histo ric channels are reoccupied on the historic floodplains, can decrease the duration of dry season basefl ow by (a) raising the alluvial water table and therefore increasing losses to evapotranspiration and (b) decreasing the hydraulic gradient and therefore the flux of water from the alluvial aquifer to the channel.

ADDITIONAL LITERATURE CITED (i.e., literature cited in this review not already cited in the document)
Bedford, B.L., and E.M. Preston. 1988. Developing the scien tific basis for assessing cumulative effects of wetland loss and degradation on landscape functions: Status, perspectives, and prospects. Environmental Management 12:751-771.
Born, S.M., S.A. Smith, and D.A. Stephenson. 1979. The hyd rologic regime of glacial terrain lakes. Journal of Hydrology 43:7–44. Bull, W.B. 1991. Geomorphic Response to Climate Change. Oxfo rd University Press, New York.
Childers, D.L., and J.G. Gosselink. 1990. Assessment of cu mulative impacts to water quality in a forested wetland landscape. Journal of Environmental Quality 19:455–464.
Dabney, S.M., L.D. Meyer, W.C. Harmon, C.V. Alonso, and G.R. Foster. 1995. Depositional patterns of sediment trapped by grass hedges. Transactions of the Ameri can Society of Agricultural Engineers 38:1719–1729.Mark C. Rains, Ph.D.

77 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE Dynesius, M., and C. Nilsson. 1994. Fragmentation and flow regu lation of river systems in the northern third of the world. Science 266:753–762. Fleckenstein, J., M. Anderson, G. Fogg, and J. Mount. 2004. M anaging surface water-groundwater to restore fall flows in the Cosumnes River. Journal of Water Resour ces Planning and Management 130:301–310.
Freeman, M.C., C.M. Pringle, and C.R. Jackson. 2007. Hydrolog ic connectivity and the contribution of stream headwaters to ecological integrity at regional sca les. Journal of the American Water Resources Association 43:5–14.
Kish, G.R., C.E. Stringer, M.T. Stewart, M.C. Rains, and A.E. Torres. 2010. A geochemical mass-balance method for base-flow separation, upper Hillsborough River wa tershed, west-central Florida, 2003-2005 and 2009. U.S. Geological Survey Scientific Investigations Repo rt 2010–5092. U.S. Government Printing Office, Washington, DC. Haitjema, H.M., and S. Mitchell-Bruker. 2005. Are water t ables a subdued replica of the topography? Ground Water 43:781–786.
Hammersmark, C.T., M.C. Rains, and J.F. Mount. 2008. Qu antifying the hydrologic effects of stream restoration in a montane meadow environment. River Research a nd Applications 24:735–753.
Haan, C.T., and H.P. Johnson. 1968. Hydraulic model of runoff from depressional areas, I: General considerations. Transactions of the American Society of A gricultural Engineers 11:364–367. Hill, A.R. and D.J. Lymburner. 1998. Hyporheic zone chemistry a nd stream-subsurface exchange in two groundwater-fed streams. Canadian Journal of Fisheries and Aquatic Sciences 55:495–506.
Hill, A.R., C.F. Labadia, and K. Sanmugadas. 1998. Hyporhei c zone hydrology and nitrogen dynamics in relation to the streambed topography of a N-rich stream . Biogeochemistry 42:285–310.
Holloway, J.M., and R.A. Dahlgren. 2001. Seasonal and event -scale variations in solute chemistry for four Sierra Nevada catchments. Journal of Hydrology 250:106–121.
Hubbard, D.E., and R.L. Linder. 1986. Spring runoff retention in prairie pothole wetlands. Journal of Soil and Water Conservation 41:122–125.
Johnson, A.I. 1967. Specific yield - compilation of specific yie lds for various materials. U.S. Geological Survey Water-Supply Paper 1662-D. U.S. Government Printing Offic e, Washington, DC. Johnston, C.A. 1994. Cumulative impacts to wetlands. Wetlands 14: 49–55.
Lee, L.C., and J.G. Gosselink. 1988. Cumulative impacts on w etlands: Linking scientific assessments and regulatory alternatives. Environmental Management 12:591–602.
Mahoney, J.M., and S.B. Rood. 1998. Streamflow requirements for cottonwood seedling recruitment—an integrative model. Wetlands 18:634–645.
McBride, J.R., and J. Strahan. 1984. Establishment and surv ival of woody riparian species on gravel bars of an intermittent stream. American Midland Naturalist 112:235–245. McCuen, R.H. 2005. Hydrologic analysis and design, 3/E. Prenti ce-Hall, Upper Saddle River, New Jersey.Mark C. Rains, Ph.D.

78 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE Meyer, L.D., S.M. Dabney, and W.C. Harmon. 1995. Sediment-tr apping effectiveness of stiff-grass hedges. Transactions of the American Society of Agricultural Engi neers 38:809–815. Murphy, K.E., M.C. Rains, M.G. Kittridge, M. Stewart, a nd M.A. Ross. 2008. Hydrological connectivity between clay settling areas and surrounding hydrological lands capes in the phosphate mining district, peninsular Florida, USA. Journal of the American Water Re sources Association 44:980–995.
Nadeau, T.L., and M.C. Rains. 2007. Contribution of headwaters to downstream integrity: Introduction to the JAWRA special issue. Journal of the American Water Res ources Association 43:1–4. Parenteau, P. 2004-2005. Bad calls: how Corps' Districts are m aking up their own rules of jurisdiction under the Clean Water Act. Vermont Journal of Environmental Law 6. http://www.vjel.org/journal/VJEL10019.html

. Peterjohn, W.T., and D.L. Correll. 1984. Nutrient dynamics i n an agricultural watershed: observations on the role of a riparian forest. Ecology 65:1466–1475.
Pringle, C.M. 2001. Hydrologic connectivity and the management o f biological reserves: a global perspective. Ecological Applications 11:981–998.
Pringle, C.M. 2003a. The need for a more predictive understanding of hydrologic connectivity. Aquatic Conservation 13:467–471.
Pringle, C.M. 2003b. What is hydrologic connectivity and why is i t ecologically important? Hydrological Processes 17:2685–2689.
Rains, M.C. 2011. Water sources and hydrodynamics of closed-ba sin depressions, Cook Inlet Region, Alaska. Wetlands 31:377–387. Rains, M.C., and J.F. Mount. 2002. Origin of shallow ground w ater in an alluvial aquifer as determined by isotopic and chemical procedures. Ground Water 40:552–563.
Richardson, J.L., L.P. Wilding, and R.B. Daniels. 1992. Recharge and discharge of groundwater in aquic conditions illustrated with flownet analysis. Geoderma 53:65–78.
Scott, M.L., J.M. Friedman, and G.T. Auble. 1996. Fluvial pro cess and the establishment of bottomland trees. Geomorphology 14:327–339.
Shaftel, R., R. King, and J. Back. 2012. Alder cover drives nitrogen availability in Kenai lowland headwater streams, Alaska. Biogeochemistry 107:135–148.
Sinclair, W.C. 1977. Experimental Study of artificial rec harge possibilities in northwest Hillsborough County, Florida. U.S. Geological Survey Water-Resources Investigat ions 77-13. U.S. Geological Survey, Tallahassee, Florida.
Sloan, C.E. 1972. Ground-water hydrology of prairie potholes i n North Dakota. U.S. Geological Survey Professional Paper 585-C. U.S. Government Printing Office , Washington.
Stanford, J.A., F.R. Hauer and J.V. Ward. 1988. Serial discontinuity in a large river system. Verh. Internat. Verein. Limnol. 23:111–1118.Mark C. Rains, Ph.D.

79 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE Stanford, J.A. and J.V. Ward. 2001. Revisiting the serial discontinuity concept. Regulated Rivers: Research and Management 17:303–310. Sumner, D.M. 2007. Effects of capillarity and microtopograph y on wetland specific yield. Wetlands 27:693– 701.
Tate, K.W., R.A. Dahlgren, M.J. Singer, B. Allen-Diaz, and E.R. Atwill. 1999. Timing, frequency of sampling affect accuracy of water-quality monitoring. Cali fornia Agriculture 53:44–48.
Tihansky, A.B. 1999. Sinkholes, west-central Florida. Pp. 121-140 in D. Galloway, D.R. Jones, and S.E. Ingebritsen (eds.), Land subsidence in the United States. U. S. Geological Survey Circular 1182. U.S. Government Printing Office, Washington, DC.
Tockner, K., F. Malard, and J. V. Ward. 2000. An extension of the flood pulse concept. Hydrological Processes 14:2861–2883. Toth, J. 1963. A theoretical analysis of groundwater flow in small drainage basins. Pp. 75–96 in Proceedings of Hydrology Symposium No. 3, Groundwater, Queen’s Printer, Ottawa, Canada.
Triska, F.J., J.H. Duff, R.W. Sheibley, A.P. Jackman, and R.J. Avanzino. 2007. DIN retention-transport through four hydrologically connected zones in a headwater catchm ent of the upper Mississippi River. Journal of the American Water Resources Association 43:60–71.
Ward, J.V. and J.A. Stanford. 1995. The serial discontin uity concept: extending the model to floodplain rivers. Regulated Rivers: Research and Management 10:159–168.
Wolman, M.G., and J.P. Miller. 1960. Magnitude and freque ncy of forces in geomorphic processes. Journal of Geology 68:54–74.John S. Richardson, Ph.D.

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### Additional Comments Submitted by Dr. John S. Richardson

Post-meeting comments It seems that there is a need to go beyond connectivity, to include aspects of the effects downstream. This was made clearer during the meeting. It also clarified why the re were sections of the charge questions that seemed more about the aggregate effects downstream, particularly question #4. This topic is not well covered in the report, and a separate section on downstream effects woul d be warranted. The connectivity aspects do not try to address the magnitudes of effect sizes. Along with the discussion of effects, the nature of those effects, and especially cumulative effects, needs to be elaborated. After the fact, I realized that the title “Connectivit y...” in the report and all the workshop documentation led me to focus on the connections and not the effects. Given that the 1 st , 2 nd

and 4 th charge questions seem to be about consequences downstream, perhaps that should be better reflected in the title. It would cert ainly have drawn our attention more specifically to the quantification of effects.
As discussed in the meeting on the 30 th January, the confusion over floodplain versus riparian needs to be clarified. Likewise, the category of non-floodplain wet lands needs more refinement as it covers an enormous range of wetland types. I think that if “floodplain” equa ls “riparian” in this scheme, then the use of floodplain should suffice. I found the use of “riparian” was not in li ne with what I consider to be riparian, but then it needs defining either way.
The executive summary needs to be shortened. As currently written it is rather long. I cannot determine who would read such a long summary. I know the document is inte nded for a broad readership, but perhaps a single page for the executive summary, and then the synthesis in the end of the document might cover all the rest of what is currently in the executive summary.
A brief section outlining uncertainties would be helpful. Pe rhaps that could go into an expanded chapter 6. This could provide a useful focal point for research to be done, or simply to provide an alert as to what we have less confidence in saying as a scientific community. It is reasonable to acknowledge that there remain uncertainties around the science.
The final section should be a synthesis and have some decl arative statements, such as are included in the charge questions. The current 6 pages of chapter 6 seems i nsufficient compared to the enormous detail of the remainder of the document.

Here are some additional references, from those that addr ess spatially structured populations of amphibians in wetlands, to papers about effects from streams to estuarie s, resource subsidies, and large-scale transformations of carbon along freshwater networks. The Naiman et al. ( 2000) reference includes the curves from the FEMAT (1993) exercise showing how different functions link up ri parian areas with water.John S. Richardson, Ph.D.

82 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE Additional references
Cole J. J., Y.T. Prairie, N. F. Caraco, W. H. McDowe ll, L. J. Tranvik, R. G. Striegl, C. M. Duarte, P. Kortelainen, J. A. Downing, J. J. Middelburg, J. Melack. 2007. Plumbing the global carbon cycle: Integrating inland waters into the terrestrial carbon budget

. Ecosystems 10: 171-184 Richardson, J.S., Y. Zhang & L.B. Marczak. 2010. Resource subsidies across the land-freshwater interface and responses in recipient communities. River Research and Applications 26:55-66.
Sakamaki, T., J.Y.T. Shum & J.S. Richardson. 2010. Waters hed effects on chemical properties of sediment and primary consumption in estuarine tidal flats: importa nce of watershed size and food selectivity by macrobenthos. Ecosystems 13:328-337.
Sakamaki, T. & J.S. Richardson. 2008. Retention, breakdown and biological utilisation of deciduous tree leaves in an estuarine tidal flat of southwestern Britis h Columbia, Canada. Canadian Journal of Fisheries and Aquatic Sciences 65:38-46.
Naiman, R.J., R.E. Bilby and P. Bisson. 2000. Riparian ecol ogy and management in the Pacific coastal rain forest. BioScience . 50:996-1011.
Werner E.E. et al., 2007. Turnover in an amphibian metacomm unity: the role of local and regional factors. Oikos 116:1713-1725 DOI: 10.1111/j.2007.0030-1299.16039.x
Hecnar SJ and MCloskey RT. 1996. Regional dynamics and the s tatus of amphibians. Ecology 77:2091-2097 DOI: 10.2307/2265703Joel W. Snodgrass, Ph.D.

83 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE 

### Additional Comments Submitted by Dr. Joel W. Snodgrass

Minor notes and typos Lines 794-794: should also include connection of floodplain wetlands to each other as a critical function of overbank flow. Many species are found associated only with fl oodplain wetlands and depend on overbank flows to connect floodplain wetlands for dispersal.
Line 826: delete “has”—should be “This water can alter ge omorphology...”
Line 900: replace colon with period.
Line 998: add “is”—should be “...the entire river system is diffi cult.”
Lines 1445-1453: this paragraph describes a study, but does not repor t the findings, leaving the reader wondering about the importance of the study.
Lines 1458-1459: given the sheer number of potholes and other types of geographically isolated wetlands it is unlikely we will ever know conditions at even a moderate fractio n of these systems. Does this mean we cannot draw any conclusions regarding these systems?
Line 1646: no paragraph needed here
Line 1677: delete “s” from “recharges”—should be “...ephemeral st reams recharge groundwater...”Lines 2066-2067: tighten—for example, “Mulholland et al. (2008) estimated that small streams ...”

Lines 3933-3934: revise to read “... when connections between wetlands and surface waters are present.”
Lines 2347-2348: flow—“... Los Alamos Canyon resulting from untreated discharge, and less than 2% ...”

Line 7040: no volume number for this reference.

Literature cited
Butler, D. R., and G. P. Malanson. 2005. The geomorphic inf luences of beaver dams and failures of beaver dams. Geomorphology 71:48-60.
Brooks, R. T., and E. A. Colburn. 2011. Extent and channel morphol ogy of unmapped headwater stream segments of the Quabbin Watershed, Massachusetts. Journal of the American Water Resources Association 47:158-168. DOI: 10.1111/j.1752-1688.2010.00499.x
Dieterich, M., and N. H. Anderson. 2000. The invertebrate faun a of summer-dry streams in Western Oregon. Archives fur Hydrobiologie 147:273-295.
Fend, S.V., and R.O. Brinkhurst. 2000. New species of Rhynchelm is (Clitellata, Lumbriculidae), with observations on the Nearctic species. Hydrobiologia 428:1-59.Joel W. Snodgrass, Ph.D.

84 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE Fend, S.V., and D.L. Gustafson. 2001. A new lumbriculid genus and species from North America (Clitellata, Lumbriculidae). Hydrobiologia 463:13-22. Naiman, R.J., C. A. Johnston, and J. C. Kelley. 1988. Al teration of North American streams by beaver. BioScience 38:753-762.
Naiman, R. J., G. Pinay, C. A. Johnston, and J. Past or. 1994. Beaver influences on the long-term biogeochemical characteristics of a Boreal Forest draina ge network. Ecology 75:905-921.
Paller, M. H. 1994. Relationships between fish assemblage st ructure and stream order in South Carolina Coastal Plain streams. Transactions of the American F isheries Society 123:150-161.
Paul, M. J., and J. L. Meyer. 2001. Streams in the urban la ndscape. Annual Review of Ecology and Systematics 32:333–365.
Peterman, W., J. Crawford & R. Semlitsch. 2008. Productiv ity and significance of headwater streams: population structure and biomass of the black-bellied salama nder (Desmognathus quadramaculatus). Freshwater Biology 53:347–357.
Pollock, M. M., M. Heim, D. Werner. 2003. Hydrologic and geomorphic effects of beaver dams and their influence on fishes. American Fisheries Society Symposiu m 37:213-233.
Roy, V., M. Amyot, and R. Carignan. 2009. Beaver ponds incre ase methylmercury concentrations in Canadian Shield streams along vegetation and pond-age gradients. Envir onmental Science & Technology 43:5605–5611.
Snodgrass, J. W. 1997. Temporal and spatial dynamics of be aver-created patches as influenced by management practices in a southeastern landscape. Journal of Applied Ecology 34:1043-1056. Snodgrass J., Forester D., Lahti M. & Lehman E. 2007. Dusky salamander (Desmognathus fuscus) nest-site selection over multiple spatial scales. Herpetologica, 63:441 –449.
Snodgrass, J. W., M. J. Komoroski, A. L. Bryan Jr., an d J. Burger. 2000. Relationships among isolated wetland size, hydroperiod and amphibian species richness : implications for wetland regulations. Conservation Biology 14:414-419.
Snodgrass, J. W., and G. K. Meffe. 1998. Influence of beave rs on stream fish assemblages: effects of pond age and watershed position. Ecology 79:928–942.
Stevens, C. E., C. A. Paszkowski, G. Scrimgeour. 2006. Older i s better: beaver ponds on boreal streams as breeding habitat for the wood frog. Journal of Wildlife Man agement 70:1360–1371. Walsh, C. J., A. H. Roy, J. W. Feminella, P. D. Cott ingham, P. M. Groffman, & R. P. Morgan. 2005. The urban stream syndrome: current knowledge and the search for a c ure. Journal of the North American Benthological Society 24:706-723.
Wellborn, G. A., D. K. Skelly, and E. E. Werner. 1996. Mechanisms creating community structure across a freshwater habitat gradient. Annual Review of Ecology and S ystematics 27:337-363.
Wiggins, G. B., R. J. MacKay, and I. M. Smith. 1980. Evoluti onary and ecological strategies of animals in annual temporary pools. Archives fur Hydrobiologia 58(supplement) :97-206.Joel W. Snodgrass, Ph.D.

85 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE Post-Meeting Comments As a general comment concerning the conceptual model introduced a t the beginning of the document I think it would be a good idea to introduce both dimensions of time a nd space and link them to the ideas of sources, sinks, refuges, lags, and transformation. What we real ly have is a hill-slope to downstream river gradient where things that at the very top of a watershed (i.e., st reams and wetlands) are more distantly removed from larger rivers downstream. In a sense the isolation of thes e headwaters and wetlands in the top of the watershed makes them sites of significant lag (e.g., water storag e) and therefore potential transformation (could also be thought of as reduced spiraling length if the concept is applie d to the entire gradient). Because streams and wetlands are most spatially removed from larger rivers, th eir individual effects will be relatively smaller and take longer periods of time to measure. However, the cumulat ive effect of their loss will be greater than closer streams and wetlands over the long-term. These connections bet ween scales of time, space and the impacts of disturbance are discussed extensively in Delcourt et al. (1983) . The development of the conceptual model in this way would allow the logical extension of the review to include the arguments presented earlier on the impacts of impervious surfaces and agricultural land conver sion discussed in my original comments.
On a related note to the development of the conceptual view, s ome changes to table 3-1 would help with clarity. I do like the idea of not having a specific sequenc e of wetland, stream, and river. Yes, larger rivers are usually downstream (but may not be when rivers enter deserts), but wetlands and streams can occur in a sequence or be close to or relatively far removed from la rge rivers. The examples I would cite here are adventitious streams verse true headwater streams (See Os born and Wiley’s work that you currently cite) and channel wetlands along stream corridors (see Webster et a l., 1996; Kratz et al., 1997; Magnuson et al., 1998; Baines et al., 2000; Riera et al., 2000; Webster et al., 2000 f or an example in Wisconsin lakes, which are formed in the same way pothole wetlands are formed). Sor anno et al. (1999) also argues for the connection between wetlands, lakes and streams based on water chemist ry in these same systems. Despite the intentions of the authors’ use of arrow in table 3-1, the arrows should be removed as they give the impression of an upstream/downstream gradient.
As far as the question concerning terminology for “geographic ally isolated wetlands,” it might be best to focus the terminology on the hill slope-downstream river gradient. Channel origin wetlands should really be considered floodplain wetlands, as they are directly adjac ent to a stream. The definition of floodplain wetlands would be those wetlands that occur on the floodplain of ri ver systems (as defined by hydrology) or located within or directly adjacent to stream channels or lakes. By the way, the lake situation is completely ignored in the document. This group of wetlands would then include beaver ponds, channel origin wetlands, and wetlands and small lakes situated along stream channel (not necessar ily acting as an origin of the channel). This would be more inclusive. Then you could have hill-slope wetlands replace the non-floodplain channel origin group. Hill-slope wetlands are wetlands that are not located directly adjacent to streams and lakes or on the floodplains of rivers. This would still be a very diverse g roup of wetlands with a range of connectivity, but would be much less confusing. I think the intent is to convey the idea that for some hill-slope wetlands we do know something about connectivity, but for other we do not.
Finally, Catherine Pringle’s work in tropical streams pr ovides another example of the influence of connectivity of low-land rivers to headwater streams on community product ion and structure, which should transfer into altered downstream influences (although I don’t think here wo rk measured this specifically). References are Pringle et al., 1993, 1999; Pringle and Blake, 1994; Pringle, 1996; Crow l et al., 2001; March et al., 2001, 2002.Joel W. Snodgrass, Ph.D.

86 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE Literature cited
Baines SB, Webster KE, Kratz TK, Carpenter S, Magnuson JJ . 2000. Synchronous behavior of temperature, calcium and chlorophyll in lakes of northern Wisconsin.. Ecol ogy. 81:815-25.
Crowl TA, McDowell WH, Covich AP, Johnson SL. 2001. Freshw ater shrimp effects on detrital processing and nutrients in a tropical head-water stream. Ecology 82: 775–783.
Delcourt, H. R., P. A. Delcourt, and T. Webb. 1983. Dynamic plant ecology: the spectrum of vegetation change in space and time. Quarterly Science Review 1:153-175. Kratz TK, Webster KE, Bowser CJ, Magnuson JJ, Benson BJ. 1997. The influence of landscape position on lakes in northern Wisconsin. Freshwater Biology. 37:209-17.
March JG, Benstead JP, Pringle CM, Ruebel MW. 2001. Linking shrimp assemblages with rates of detrital processing along an elevational gradient in a tropical st ream. Canadian Journal of Fisheries and Aquatic Sciences 58: 470–478.
March JG, Pringle CM, Townsend MJ, Wilson AI. 2002. Effect s of freshwater shrimp assemblages on benthic communities along an altitudinal gradient of a tropical isl and stream. Freshwater Biology 47: 377–390.
Pringle CM. 1996. Atyid shrimps (Decapoda: Atyidae) influen ce the spatial heterogeneity of algal communities over different scales in tropical montane strea ms, Puerto Rico. Freshwater Biology 35: 125–140.
Pringle CM, Blake GA, Covich AP, Buzby KM, Finley A. 1993. Eff ects of omnivorous shrimp in a montane tropical stream: sediment removal, disturbance of sessile invertebrates and enhancement of understory algal biomass. Oecologia 93: 1–11.
Pringle CM, Blake GA. 1994. Quantitative effects of atyid s hrimp (Decapoda: Atyidae) on the depositional environment in a tropical stream: use of electricity for e xperimental exclusion. Canadian Journal of Fisheries and Aquatic Sciences 51: 1443–1450.
Pringle CM, Hemphill N, McDowell WH, Bednarek A, March JG. 1999. Linking species and ecosystems: different biotic assemblages cause interstream difference s in organic matter. Ecology 80: 1860–1872.
Riera JL, Magnuson JJ, Kratz TK, Webster KE. 2000. A geomorphi c template for the analysis of lake districts applied to Northern Highland Lake District, Wisconsin, U.S. A.. Freshwater Biology. 43:301-18.
Soranno PA, Webster KE, Riera JL, Kratz TK, Baron JS, Bukaveckas PA, Kling GW, White DS, Caine N, Lathrop RC et al.. 1999. Spatial variation among lakes wi thin landscapes: ecological organization along lake chains.. Ecosystems. 2:395-410.
Webster KE, Soranno PA, Baines SB, Kratz TK, Bowser CJ, Dillon PJ, Campbell P, Fee EJ, Hecky RE. 2000. Structuring features of lake districts: landscape controls on lake chemical responses to drought. Freshwater Biology. 43:499-515.
Webster, K.E., T.K. Kratz, C.J. Bowser, J.J. Magnuson, and W.J. Rose. 1996. The influence of landscape position on lake chemical responses to drought in northern Wi sconsin, USA. Limnol. Oceanogr. 41:977-984.Arnold van der Valk, Ph.D.

87 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE 

### Additional Comments Submitted by Dr. Arnold van der Valk

Some Additional Comments
The main purpose of this report is to demonstrate the connect ivity between streams and wetlands and navigable rivers. There are a large number of papers tha t have been published in the landscape ecology literature on connectivity and how to measure it. This liter ature is largely ignored in this report. A review of what is meant by connectivity and the various relevant wa ys in which streams and wetlands may be linked to rivers is needed. In fact, the whole report might have been more usefully organized around various kinds of linkages with chapters on surface water flows, groundwater flows, wind, and various animals vectors and their relative influences on navigable rivers. One of the major dilemmas facing the reviewers was that hydrological linkages are better studied and thus are much ea sier are to demonstrate than biological linkages. Not surprisingly the report emphasizes hydrological connectivi ty. Biological linkages are often sporadic and highly species specific and are thus harder to document. Most of the focus on biological connectivity in the report is on fish movements into and out of wetlands on floodpla ins. Because isolated wetlands are linked to rivers primarily by biological linkages, I believe that this report seriously underestimates the connectivity between isolated wetlands and rivers. The literature on waterbird (ducks, geese, cranes, etc.) migratory and local movements, which is largely ignored in the report, is full of accounts of birds moving from wetlands to rivers and vice versa, e.g., Canvasbacks in the Mississi ppi River flyway. In the case study on prairie potholes, however, there is a good synthesis of the evidence for both hydrological and biological connectivity of potholes to rivers. In short, I think that a stronger case can be made that some of the wetlands in the isolated wetland category are connected to rivers.
I found the Non-Riparian and Channel Origin (NRCW) class of wetlands created in this report unnecessary and confusing. In fact, the term NRCW is never used in the Executive Summary. For the most part, this term is used a catchall for non-riparian/non-floodplain wetlands. The common denominator that supposedly justifies putting prairie potholes and other isolated wetlan ds in the same class as wetlands that are the headwaters for streams (channel origin wetlands) is unidirec tional surface flow (P. 42, ll. 813-815). Although some isolated wetlands like prairie potholes during high wat er events do have temporary surface connections to each other and even to nearby streams, many do not as n oted. Many headwater wetlands, however, can have water backing up into them from streams during flooding e vents. It would be simpler to eliminate the use of the NRCW class from the report. The problem with l umping these two types of wetlands together is illustrated on P. 206 ll. 4292-4294: “NRCWs, however, are generally farther from stream channels than riparian/floodplain wetlands, which make hydrologic connectivity much less frequent, if present at all.” This statement is by definition untrue for channel origin wetlan ds.

Instead of the artificial NRCW class of wetlands, it would be more useful to follow the Cowardin et al. (1979) classification of wetlands which distinguishes five basic types (systems) of wetlands, only three of which are relevant in this context, (riverine, palustrine, and lacustr ine). As defined by Cowardin et al. (1979), “The term SYSTEM refers here to a complex of wetlands and deepwater h abitats that share the influence of similar hydrologic, geomorphologic, chemical, or biological factors.” Co wardin et al., recognize that intermittent streams are connected to perennial reaches of streams. The y are treated as part of the riverine system. Lacustrine wetlands are found along the peripheries of lakes , and there is absolutely no doubt that they are connected to navigable water. What is being examined in this report is the connectivity between rivers andArnold van der Valk, Ph.D.

88 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE various kinds of palustrine wetlands. Palustrine wetlands are bounded by uplands. There are many kinds of palustrine wetlands, and they are found “shoreward of lakes, river channels, or estuaries; on river floodplains; in isolated catchments; or on slopes.” In other words , this report should focus on the connectivity of different kinds of palustrine wetlands. This ranges from those clearl y linked to rivers like palustrine wetlands on floodplains to those with much weaker linkages like palustrine wetlands in isolated catchments like many inter-mountain wetlands. In the case of palustrine wetla nds that generally have no surface water connections to rivers, each major type should be treated separately (prairie potholes, California vernal pools, Carolina bays, Texas playas, etc.)
The Cowardin et al., classification systems is used by t he National Wetland Inventory. Discussing the connectivity of palustrine wetlands to rivers would make it i mmediately obvious to readers familiar with wetlands what this report is trying to do, and it would link the report more directly to the existing wetland literature.
Five functions of streams and wetlands are recognized (P. 5, ll. 106-113). I would suggest renaming the last one, Lag, Desynchronization. A lag is an effect, not a fu nction.
What is the relative importance of hydrological vs. biologic al connectivity? It is possible for some types of wetlands to have no surface water connection to streams. Gi ven that all wetlands have hydric plants and a host of aquatic animals (invertebrates, birds, mammals, m icroorganisms, etc.), even hydrologically isolated wetlands are never isolated biologically. What species should count in establishing biological connectivity? In the report, all microorganisms (algae, bacteria, fungi, protozoans, etc.) are essentially ignored. Although the report does a good job in demonstrating the ubiquity of biological connectivity, it is unclear how important this type of connectivity is when compared to hydrological connect ivity and what minimum criterion or threshold is required to demonstrate biological connectivity. Doe s demonstrating the one-time movement or dispersal of one species from a river or a stream to a h ydrologically isolated wetland (or vice versa) mean that the “isolated” wetland is not really isolated? If just e stablishing some kind of biological linkage between a wetland and a river establishes connectivity, then there is no such thing as an isolated wetland.
When looking for linkages between “isolated” wetlands and ri vers, a landscape approach is needed. One possible way to examine these linkages would be to use an H GM approach to estimate water, sediment, nutrient, etc. storage by the wetlands in a watershed and thus not entering the rivers. Potential linkages of various animal groups and wind could also be explored using t his general approach. The more linkages that can be demonstrated the greater the influence of isolated w etlands in a watershed (or other comparable landscape unit) on the rivers in it.
In summary, the authors of the report focus primarily on s urface water flows as the major link between rivers and streams and wetlands. This primarily unidirectional f low of water into rivers is easy to demonstrate and its importance can be quantified. The more complex and often sporadic and bidirectional linkages caused by wind and movement of organisms are noted, but their influ ence on navigable waters has rarely been documented. Whether such movements are essential for the pers istence of some organisms in rivers is unknown. That some organisms (some waterfowl, some mammals, and some amphibians) use both rivers and isolated wetlands during their life cycles is known. As a c onsequence, in any landscape all bodies of water are interconnected and influence each other, but these interact ions are often sporadic and asymmetrical.Mark S. Wipfli, Ph.D.

89 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE 

### Additional Comments Submitted by Dr. Mark S. Wipfli

Marine-derived nutrient effects on stream productivity
Discussed at the review on 30 Jan, 2012 was the topic of mar ine-derived nutrients, and their effects on headwater productivity in places that receive runs of anadrom ous fishes. It was suggested that a discussion of this topic be included in the report, and I agree tha t it should be included. This phenomenon is demonstrated through runs of adult Pacific salmon throughout the west co ast of North America, but occurs along the east coast with Atlantic salmon, as well as runs of shad, lamprey, and other species, and throughout other parts of the world. Spawning adults deliver nutrients and carbon from t he ocean when they return to fresh water to spawn (and die). This subsidy of nutrients and carbon (energy ) from the ocean has been universally shown to increase stream productivity, including in headwater stre ams, at multiple trophic levels (periphyton, aquatic invertebrates, and fishes). The increased production in headwa ters in turn provides more invertebrates that can get flushed downstream from smaller headwater channels to downstream waters. Thus, the ocean is connected to headwaters via the movement of marine subsidies in to watersheds. In turn a portion of this invertebrate production can subsequently get delivered downstre am from headwaters.
Here are some of my papers on this topic. They in turn con tain numerous additional citations on the subject that can be included in the report, if EPA decides this is a topic worth including.
Wipfli, M.S., J.P. Hudson, J.P. Caouette, N.L. Mitchell , J.L. Lessard, R.A. Heintz, and D.T. Chaloner. 2010. Salmon carcasses increase stream productivity more than i norganic fertilizer pellets: A test on multiple trophic levels in streamside experimental channels. Trans actions of the American Fisheries Society 139: 824-839.
Heintz, R.A., M.S. Wipfli, and J.P. Hudson. 2010. Identifica tion of marine-derived lipids in juvenile coho salmon and aquatic insects through fatty acid analysis. Transactions of the American Fisheries Society 139: 840-854.
Lang, D.W., G.H. Reeves, D.D. Hall, and M.S. Wipfli. 2006. The influence of fall-spawning coho salmon (Oncorhynchus kisutch) on growth and production of juvenile coho sa lmon rearing in beaver ponds on the Copper River Delta, Alaska. Canadian Journal of Fis heries and Aquatic Sciences 63: 917-930.
Hicks, B.J., M.S. Wipfli, D.W. Lang, and M.E. Lang. 2005. Marine-derived nitrogen and carbon in freshwater-riparian food webs of the Copper River Delta, so uthcentral Alaska. Oecologia 144: 558-569.
Heintz, R.A., B.D. Nelson, J.P. Hudson., M. Larsen, L. Holland, and M.S. Wipfli. 2004. Marine subsidies in freshwater: Effects of salmon carcasses on the lipid c lass and fatty acid composition of juvenile coho salmon. Transactions of the American Fisheries Society. 133: 559-567.
Wipfli, M.S., J.P. Hudson, J.P. Caouette, and D.T. Cha loner. 2003. Marine subsidies in freshwater ecosystems: salmon carcasses increase the growth rates of stream-resident salmonids. Transactions of the American Fisheries Society. 132: 371-381.Mark S. Wipfli, Ph.D.

90 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE Wipfli, M.S., J.P. Hudson, and J.P. Caouette. 1998. Influence of salmon carcasses on stream productivity: response of biofilm and benthic macroinvertebrates in southeas tern Alaska, USA. Canadian Journal of Fisheries and Aquatic Sciences. 55: 1503-1511.

Some additional relevant MDN papers include:
Bilby, R. E., B. R. Fransen, P. A. Bisson, and J . K . Walter. 1998. Response of juvenile coho salmon (Oncorhynchus kisutch) and steelhead (Oncorhynchus mykiss) to the addition of salmon carcasses to two streams in southwestern Washington, USA. Canadian Journal of Fisheries and Aquatic Sciences 55:1909-1918.
Bilby, R. E., Fransen, B. R., Walter, J . K., Cederho lm, C. J ., and W. J . Scarlett. 2001. Preliminary evaluation of the use of nitrogen stable isotope ratios to e stablish escapement levels for Pacific salmon. Fisheries 26:6-14.
Claeson, S. M., J. L. Li, J. E. Compton, and P. A. Bis son. 2006. Response of nutrients, biofilm, and benthic insects to salmon carcass addition. Canadian Journal of Fisheries and Aquatic Sciences 63:1230-1241.
Jonsson, B., and N. Jonsson. 2003. Migratory Atlantic salm on as vectors for the transfer of energy and nutrients between freshwater and marine environments. Freshwa ter Biology 48:21-27.
Nislow, K.H., and B.E. Kynard. 2009. The role of anadromo us sea lamprey in nutrient and material transport between marine and freshwater environments. Amer. Fish Soc. Symp. 69:485-494.
Rand, P. S., C. A. S. Hall, W. H. McDowell, N. H. R ingler, and J. G. Kennen. 1992. Factors limiting primary productivity in Lake Ontario tributaries receiving salmon m igrations. Canadian Journal of Fisheries and Aquatic Sciences 49:2377-2385.

Terrestrial prey subsidies
Another topic briefly discussed for possible inclusion in the final report was the trophic linkage between headwater streams and their riparian forests, and how this linkage affects the flow of terrestrial invertebrates from headwater streams to downstream habitats. This is an other avenue thorough which headwater streams are connected to downstream waters. Below are a few refe rences for the report that discuss terrestrial invertebrate subsidies to streams, which in turn contain furt her references the authors of the EPA report can decide on their inclusion.
Allan, J. D., M. S. Wipfli, J. P. Caouette, A. Prussia n, and J. Rodgers. 2003. Influence of streamside vegetation on inputs of terrestrial invertebrates to salmonid food webs. Canadian Journal of Fisheries and Aquatic Sciences 60:309-320.
Baxter, C. V., K. D. Fausch, M. Murakami, and P. L. C hapman. 2007. Invading rainbow trout usurp a terrestrial prey subsidy to native char and alter their be havior, growth, and abundance. Oecologia 153:461-470.
Baxter, C. V., K. D. Fausch, and W. C. Saunders. 2005. Tan gled webs: reciprocal flows of invertebrate prey link streams and riparian zones. Freshwater Biology 50(2):201- 220.Mark S. Wipfli, Ph.D.

91 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE Kawaguchi, Y., and S. Nakano. 2001. Contribution of terrestr ial invertebrates to the annual resource budget for salmonids in forest and grassland reaches of a headw ater stream. Freshwater Biology 46:303-316. Kawaguchi, Y., S. Nakano, and Y. Taniguchi. 2003. Terrest rial invertebrate inputs determine the local abundance of stream fishes in a forested stream. Ecology 84(3) :701-708.
Mason, C. F., and S. M. MacDonald. 1982. The input of terre strial invertebrates from tree canopies to a stream. Freshwater Biology 12:305-311.
Nakano, S., H. Miyasaka, and N. Kuhara. 1999. Terrestria l-aquatic linkages: riparian arthropod inputs alter trophic cascades in a stream food web. Ecology 80(7):2435-2441.
Richardson, J.S., Y. Zhang & L.B. Marczak. 2010. Resource subsidies across the land-freshwater interface and responses in recipient communities. River Research and Applications 26:55-66.
Saunders, W. C., and K. D. Fausch. 2007. Improved grazing man agement increases terrestrial invertebrate inputs that feed trout in Wyoming rangeland streams. Trans actions of the American Fisheries Society 136:1216-1230.A-1 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE 

## Appendix A: Individual Reviewer CommentsA-3 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE



### David J. Cooper, Ph.D. Senior Research Scientist and Professor Department of Forest and Rangeland Stewardship

Colorado State University Fort Collins, CO

Dr. David J. Cooper is a Senior Research Scientist/P rofessor in the Department of Forest and Rangeland Stewardship, Colorado State University, Fort Collins, Colorado. His expertise is plant and vegetation ecology and hydrologic processes supporting wetland and riparian e cosystems in western North America. He also has active projects in the Andes of Peru and Bolivi a, and in Slovakia and Poland in Europe. The main themes of his research are the role of hydrologic proces ses in shaping ecosystems, plant establishment processes, the role of herbivory and alternative states in ecosystems, characterization of vegetation types, invasion of exotic plants into riparian areas, and rest oration ecology. His work supports federal agencies including National Parks, National Forests, BLM, EPA, Bureau of Reclamation, and research support comes from these and other federal agencies as well as NSF, pri vate corporations, local governments, and nonprofit agencies. In the past ten years he has published 50 ar ticles in peer reviewed journals, with most appearing in Ecological Applications, Journal of Hydrology, Cana dian Journal of Botany, River Research and Applications, Journal of Vegetation Science, Biological Invasions, Plant Ecology, Arctic Antarctic and Alpine Research, Restoration Ecology, Journal of Applied E cology, Hydrogeology Journal, Oecologia, Environmental Management, Wetlands, Water Resources Researc h, Hydrological Processes, Ecosystems, Plant and Soil, Journal of Range Management, Journal of E cology, and Soil Biology and Biogeochemistry.David J. Cooper, Ph.D.

A-5 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE 

### Peer Review Meeting of EPA’s Draft Report: Connectivity of Streams and Wetlands to Downstream Waters – A Review and Synthesis of the Scienti fic Evidence

Comments submitted by Dr. David J. Cooper

Overall Comments The authors of the report have done an excellent job of bringi ng together a huge and scattered literature. The report was difficult to read due to its length, and I find it hard to imagine that most people will use this anything other than a reference document. The literature r eview indicates that our knowledge of hydrologic connections between tributary streams and wetlands and wat ers of the U.S. is conceptual, with case studies in several portions of the U.S. but large regions, such as wes tern mountains, and southwestern deserts, where little is known. A few things should be clarified to make this report more useful.
The report focuses on what we know. I would suggest that eac h section of the report must have a discussion of what is unknown or uncertainties about connections, functions, a nd what future research is needed to support our understand of these processes. The report gives the impr ession that we know most of what is needed to understand and regulate these tributaries and wetlands. I th ink this is only partially correct.
The temporal aspect of these jurisdictional identificati ons should be clarified. For example jurisdictional wetlands, under S404, must have flooding or soil saturation for a certain number of days during the growing season. One day of saturation is insufficient, but 14 days i s typically sufficient. However this report does not clarify how many hours, days, or weeks per year a tributary must flow into a water of the U.S. to be considered jurisdictional. For an ephemeral stream in Ari zona that is tributary to a water of the U.S. is it sufficient if this stream flows on average 1 or 2 days per year, and in some years never flows? For a noncontinuous wetland how often does the surface or subsurface connecti on have to occur? How often do the cited ecological functions, i.e., sediment retention, have to occur? These concepts are critical to have a definitive and objective jurisdictional approach. After the panel meeting I’m still unsure how to include every single channel across the U.S. into a single framework of ecological functioning.
Methods for measuring ecological function should be reviewed and included in this report. The U.S. has spent millions of dollars supporting the Adamus methods, Wetland Eval uation Technique, HGM and other approaches that all have been extensively peer reviewed and used in the US. I include a few key references at the end of my comments. Methods such as these are critica l for inclusion because any field activities would need a framework for how to evaluate function or nexus bet ween any stream or wetland and a downstream
water.
I understand the importance of identifying “similarly situa ted waters” as a way of extending our understanding beyond single sites. However, the geomorphic context of s uch sites must be carefully evaluated. This is no simple matter and no method for doing such comparisons is presented in the report.
The definitions used in this report need significant improvem ent. For example wetlands, riparian, floodplain, non-riparian wetland, etc. are all in need of greater cl arification. I suggest not using the Cowardin et al. (1979) definition of wetland in this report. The U.S. has regul atory definitions of wetlands that should be used asDavid J. Cooper, Ph.D.

A-6 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE these definitions have been peer reviewed innumerable times . Riparian is more a term of art than science. The classical definition is that it includes areas adjacent to flowing water, i.e., streams. I’m not sure how floodplains differ from riparian areas, or how riparian ar eas are defined or bounded.
The overall report needs an ending synthesis, not summary at the end of the document.
The example provided for Southwestern streams, the San Pe dro river is not a representative stream. Much attention has been paid to the San Pedro, making it the mo st studied stream in the SW because it is unique. It flows north from Mexico, has many perennial reaches, almos t all of the river has shallow ground water, and most has well developed riparian forests. In contrast mo st streams in the region are ephemeral, few are intermittent and only a very few are perennial. Few have shallow ground water. I would suggest that if the San Pedro is retained, than a second example system is presented. One of our published papers (Shaw and Cooper 2008) published in the Journal of Hydrology may provide a different representative ephemeral stream baseline. I have attached this in case EPA authors wish to use this or have not seen it.

CLASSIFICATION: I think that a classification of U.S. wetlands would be helpful as a unifying theme for the document. There are many attempts to classify wetlands an d regions including EPA’s ecoregion concepts from Omernick et al., in its many documents. Each region has distinctive wetland types, and it would be nice to discuss each type and issues related to connectivity, an d functions that effect downstream waters. In addition, the book on Wetlands of the U.S. should be published this spring/s ummer by University of California Press. The wetland types or chapters within could also provide a good framework for discussing issues related to connectivity, and uncertainty in connections and ecological fun ctions. Another potential is to organize around HGM wetland types, such as depression, slope, etc. alt hough there is great variance through the U.S. on how basin/depression wetland function.
Beavers are a key part of the biotic/hydrologic connection fo r streams and riparian areas throughout the northern hemisphere, and even the southern hemisphere. It would be important to mention this important driver of connections and exchange of water, materials and biota between streams and wetlands.
I also ask EPA to remove concepts suggesting that riparian areas are “transition zones”. This is completely false and misleading. Riparian zones support distinctive biota , hydrological and ecological processes that distinguish them from uplands or aquatic ecosystems.
The concept of “channel origin wetlands” is quite foreign. I think that EPAs concept was that sites of ground water discharge would support wetlands that would feed into downstream waters. However, hydrologically, many wetlands are flow through, with ground water flowing in, and ground water flowing out, and no surface water other than in the wetland. This concept is importa nt for the prairie potholes, but also anywhere else that basin wetlands are prevalent.
Many figures could use revision as listed below:
Figure 3-2, does not show ground water flow, and little of t he landscape is connected to the channels.
Figure 3-7, panel a shows a stream that virtually dries up, and it’s not very representative for perennial streams in most of the US.David J. Cooper, Ph.D.

A-7 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE Figure 3-6, all of these panels show a river connected via ground w ater inflow. Please expand these concepts to include rivers that are not connected to adjacent lands via ground water. Either they are losing, or disconnected. Same comment for Figure 3-13 and Figure 3-16.
Figure 3-5, the scale on this is very poor. For example showi ng a regional GW flow that is just a tad different from local or intermediate GW flows is inaccurate.

Technical Charge Questions

1. This report concludes that all streams, regardless of f low duration or size, are physically, chemically, and biologically connected to rivers; and these connections, individually or cumulatively, exert a strong influence on the character an d functioning of downstream waters.
a) Are these conclusions supported by the scientific evid ence? b) Does the report include the most relevant peer-reviewed literature on these topics, including evidence of connectivity and isolation? If not please indicate which references a re missing. c) Was the reviewed literature cited and summarized correc tly? If not please indicate where correction or revision is needed. The conclusions are supported in part. Clearly if hazardous waste is placed into an ephemeral desert stream, the material will likely flow to a water of the U.S. on some time scale, likely years to decades.

2. This report concludes that open water and wetlands in riparian areas and floodplains of streams and rivers are physically, chemically, and biologically connect ed with the river network, and that their functions exert a strong influence on the char acter and functioning of downstream waters.
a) Are these conclusions supported by the scientific evid ence? b) Does the report include the most relevant peer-reviewed literature on these topics, including evidence of connectivity and isolation? If not please indicate which references a re missing. c) Was the reviewed literature cited and summarized correc tly? If not please indicate where correction or revision is needed. The report provides evidence of these connections, but what is missing is some idea of how often and how long these connections must occur each year. I would also like to see a better review of the types of channels and wetlands that occur in the U.S. and which we have sufficient evidence for these connections, and which we don’t. This could be presented in a table.David J. Cooper, Ph.D.

A-8 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE 3. This report concludes that for non-riparian/non-flood plain wetlands that are not connected to the river network through a stream channel (i.e., geographical ly isolated wetlands and wetlands that spill into losing streams), connectivity and isolation vary wit hin a watershed and over time, making it difficult to generalize about their connections to, or isolation from, downstream waters. The literature we reviewed does not provide sufficient infor mation to evaluate the degree of connectivity (absolute or relative) of these non-riparian particular w etlands.
a) Are these conclusions supported by the scientific evid ence? b) Does the report include the most relevant peer-reviewed literature on these topics, including evidence of connectivity and isolation? If not please indicate which references a re missing. c) Was the reviewed literature cited and summarized correc tly? If not please indicate where correction or revision is needed. This is correct. Documented evidence of hydrologic connections from non-connected wetlands to streams is sparse, and the conditions for such connection are poorly know n. Probably the best large-scale evidence is the long-term data collected in the prairie pothole regi on by Winter et al. However few such studies occur in the western US.

4. This report concludes that while the influence of a particular stream or wetland on downstream waters might be small, the aggregate contribution by an entire class of streams or wetlands (e.g., all ephemeral streams in the river network, or a cluster of small wetlands) might be substantial.

a) Is this conclusion supported by the scientific eviden ce?

b) Does the report include the most relevant peer-reviewed literature on this topic? If not please indicate which references are missing.

c) Was the reviewed literature cited and summarized correc tly? If not please indicate where correction or revision is needed.

The contribution of streams and wetlands on downstream wate rs is well known for flood water retention (the studies by Novitski 1978 in Wisconsin should be added). Denit rification has been shown in many wetlands. However few other functions have been conclusively demonstrated for many wetland types.

Literature Cited
Novitzki, RP. 1978. Hydrologic characteristics of Wisconsin’s wetlands and their influence on floods. Pp. 377-388, in P. Greeson, J. Clark, JE Clark (eds). Wetland f unctions and values: the status of our understanding. Proc. National Symposium on Wetlands. Am Wat er Res Assoc, Minneapolis MN.
Thomas C. Winter, Judson W. Harvey, O. Lehn Franke, Willi am M. Alley. 2008. Surface and Ground water, a single Resource. USGS Circular 1139.David J. Cooper, Ph.D.

A-9 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE Hauer, F. R., B. J. Cook, M. C. Gilbert, E. C. Claira in, Jr., and R. D. Smith. 2001. The Hydrogeomorphic Approach to Functional Assessment: A Regional Guidebook for A ssessing the Functions of Riverine Floodplain Wetlands in the Northern Rocky Mountains. Speci al Publ. WES, USCOE, Vicksburg, MS. p.255.
Hauer, F. R., B. J. Cook, M. C. Gilbert, E. C. Claira in, Jr., and R. D. Smith. 2000. A regional guidebook: Assessing the functions of intermontane prairie pothole wetl ands in the northern Rocky Mountains. Special Publ. WES, USCOE, Vicksburg, MS. p.189.
THREE papers (PDFs attached) that you might consider refer encing as they present original data on hydrologic connectivity on ephemeral and intermittent streams t o riparian and wetland ecosystems
Shaw, J. and D. J. Cooper. 2008. Watershed and stream re ach characteristics controlling riparian vegetation in semiarid ephemeral stream networks. Journal of Hydrology 350:68-82.
Westbrook, C., D. J. Cooper, B. Baker. 2006

. Beaver dams and floods in controlling hydrologic processes of a mountain valley. Water Resources Research 42: W06404, doi:10.1029/2005WR004560
Wurster, F.C., D.J. Cooper, and W.E. Sanford. 2003. Stre am/aquifer interactions at Great Sand Dunes National Monument, Colorado: Influences on interdunal wet land disappearance. Journal of Hydrology 271 :77-100.A-11 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE



### William G. Crumpton, Ph.D. Associate Professor Department of Ecology, Evolution & Organismal Biology

Iowa State University Ames, IA

William Crumpton is an Associate Professor in the Depar tment of Ecology, Evolution and Organismal Biology at Iowa State University, and Chair of ISU’s Envir onmental Science and Environmental Studies programs. He obtained his B.S. (interdisciplinary scienc e) and M.S. (marine science) from the University of West Florida, his Ph.D. (limnology) from Michigan State U niversity, and spent two years as a Postdoctoral Research Associate at the U.C. Davis field station at Lake Tahoe before joining the faculty of Iowa State University.

Dr. Crumpton’s research focuses on wetland processes and functions, including the dynamics of energy flow and nutrient transformation in wetlands, the fate a nd effects of agricultural contaminants in wetlands, and the role of restored and constructed wetlands in wate rshed hydrology and water quality. His work has been funded by a broad and diverse array of sources ( including USDA, USGS, USFWS, U.S.EPA, Iowa DNR, Iowa Department of Ag. and Land Stewardship, Iowa Natural Heritage Foundation, and Ducks Unlimited ) and published in a wide range of journals ( including Wetlands, Wetlands Ecology and Management, Journal of Hydrology, Hydrobiologia, Regulated Rivers: Reasearch and Management, Water Science and Technology, Ecological Engineering, Journal of Water Pollution Control Federation, Bulletin of Environmental Contamination and Toxicology, and the Journal of Freshwater Ecology ). Much of his current work focuses on the development and application of per formance forecast models for siting, design, and assessment of wetland restorations in agricultural watersheds. This work provided the research foundation for the Iowa Conservation Reservation Enhancement Program, a ten-year, $89 million program using targeted wetland restorations to reduce nitrate loa ds from tile-drained agricultural watersheds.William G. Crumpton, Ph.D.

A-13 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE 

### Peer Review Meeting of EPA’s Draft Report: Connectivity of Streams and Wetlands to Downstream Waters – A Review and Synthesis of the Scienti fic Evidence

Comments submitted by Dr. William G. Crumpton

POST MEETING ADDITIONAL COMMENTS
My additional comments relate primarily to charge questi on 3.
Much of our panel’s discussion seemed to focus on issues rela ted to connectivity and while connectivity is important, it is in many ways more important to consi der evidence of influence. This could be especially true in the case of “geographically isolated wetlands”. In fact, the influence of “geographically isolated” wetlands could be increased by some degree of isolation, for example in the case of sediment retention and flood storage. Isolated depressional wetlands that are connec ted to downstream waters only during relatively infrequent storm flows could exert substantial influence on sediment transport and storm flows to downstream waters in part due to the relative isolation of these depressions from those downstream waters. Influence does not require a direct connection and “geographic ally isolated wetlands” could certainly alter material fluxes to downstream waters. Some of the effec ts of “geographically isolate wetlands” could be quantified based on available literature as has been done f or tributary streams (for example an estimate of the flood storage volume of isolated depressions based on published values of their areal extent (for example using the estimates of Miller et al., 2009 for Iowa).
The apparent uncertainty over the connectivity of “geographicall y isolated wetlands” could be greatly reduced and the issues clarified by using an HGM approach to explicitly considering the links between wetland soils and hydrology. Wetland soils and hydrology are inext ricably linked and soils can help in interpreting sources, pathways and frequency of water move ment through wetlands and between wetlands and downstream waters. The NRCS technical note on “Soil Hydrodynamic Interpretations of Wetlands” is a very useful resource for this.
The report needs to clearly define and discuss issues rel ated to cropped wetlands. Prior converted cropland and farmed wetlands are two distinct categories of wet land defined by the Food Security Act that have important implications with respect to both wetland pro tection and agricultural production. The 1985 Farm Bill established two categories of cropped wetlands, pri or converted cropland and farmed wetlands.
Prior converted cropland : Wetlands that had been sufficiently drained prior to December 23, 1985 are referred to as prior converted cropland and are not trea ted as wetlands under the Swampbuster provisions of the 1985 Farm Bill. There are no USDA restricti ons on further improving or enhancing drainage on prior converted cropland.

Farmed wetlands : Wetlands that had not been sufficiently drained prior to December 23, 1985 are referred to as farmed wetlands and are afforded protec tion under the Swampbuster provisions of the 1985 Farm Bill. There are restrictions on further improving or enhancing drainage on farmed wetlands. Farmers who improve the drainage of a farmed wetland beyond the “scope and effect of the originalWilliam G. Crumpton, Ph.D.

A-14 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE drainage” could lose all USDA program benefits or face p enalties. These penalties or loss of benefits can cost landowners tens- or even hundreds of thousands of do llars.
The report needs to clearly define and discuss the issues related to subsurface tile drainage and how that influences connectivity of “geographically isolated wetlands ” to downstream waters. In much of the Corn Belt, subsurface tile drainage systems transport most o f the water that leaves agricultural watersheds. For systems with surface intakes, tile drains could provide a direct connection to downstream waters. Regardless of one’s opinion over the importance of this connection, it is un acceptable to ignore this issue in a report that addresses the connectivity and influence of wetlands on down stream waters.

RESPONSE TO TECHNICAL CHARGE QUESTIONS:

1. This report concludes that all streams, regardless of f low duration or size, are physically, chemically, and biologically connected to rivers; and these connections, individually or cumulatively, exert a strong influence on the character an d functioning of downstream waters.
a) Are these conclusions supported by the scientific evidence?
b) Does the report include the most relevant peer-revie wed literature on these topics, including evidence of connectivity and isolation? If not please indicate which references a re missing.
c) Was the reviewed literature cited and summarized cor rectly? If not please indicate where correction or revision is needed.
The conclusion that all streams are physically and chemica lly connected to rivers is well supported if we incorporate a minor modification that seems consistent wi th the body of the report. Specifically, it is possible to have losing streams that are not hydrologically connected to downstream waters via channels and perhaps not chemically or biologically connected. I infe r this as the basis for the report excluding certain channel origin wetlands that feed losing streams . The exception of certain wetlands spilling to losing streams as potentially not being connected to downst ream waters is introduced in the Executive Summary on page 13, lines 285-289 and repeated numerous times throughout document.

With the exception of certain losing streams that may la ck a connection to downstream waters, the conclusion that at least collectively streams exert a st rong influence on the character and function of downstream waters is well supported. The report illustrat es this through estimates of the fractions of river flow and material loads (nutrients, carbon, etc.) that originate in streams.William G. Crumpton, Ph.D.

A-15 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE The report provides sufficient coverage of the relevant peer -reviewed literature on physical and chemical connections of streams to downstream waters with the possible exception of losing stream reaches (i.e., the possible isolation of losing reaches fr om downstream waters). Given the apparent inference in the report that certain losing stream re aches may not be connected to downstream waters, this particular concept should be clarified and supported w ith relevant literature.
In general, the literature was cited and summarized appro priately. The report does a particularly good job in summarizing the complex nature of stream networks in cluding the major components and their spatial and temporal dynamics.
I offer no response with respect to the questions involving biological connections of streams to downstream waters as this is outside my area of expertis e.

2. This report concludes that open water and wetlands in riparian areas and floodplains of streams and rivers are physically, chemically, and biologically connect ed with the river network, and that their functions exert a strong influence on the char acter and functioning of downstream waters.
a) Are these conclusions supported by the scientific evidence?
b) Does the report include the most relevant peer-revie wed literature on these topics, including evidence of connectivity and isolation? If not please indicate which references a re missing.
c) Was the reviewed literature cited and summarized cor rectly? If not please indicate where correction or revision is needed.
The conclusion that wetlands in riparian areas and floodpl ains of streams and rivers are physically, chemically, and biologically connected with the river network is well supported by the scientific evidence (with the possible exception of wetlands in ripari an areas and floodplains of certain permanently losing steams that are never connected to downstr eam waters- these systems would be rare). The report illustrates this through literature documenting the unidirectional and bidirectional transfer of water and materials and transport and mi gration of organisms.
The conclusion that wetlands in riparian areas and floodpl ains of streams and rivers exert a strong influence on the character and function of downstream wa ters is well supported by the scientific evidence – at least for the systems collectively, and th at qualification should be included in the conclusion

. The report provides sufficient coverage of the relevant peer -reviewed literature on physical, chemical connections of wetlands in riparian areas and floodplains to the stream networks. The literature was cited and summarized correctly. The report recognizes t he uncertainty in quantifying exchanges between stream/river channels and their riparian areas/floodplains and provides sufficient documentation of the transfers without extending the analyses beyond what can be re asonably concluded.William G. Crumpton, Ph.D.

A-16 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE 3. This report concludes that for non-riparian/non-flood plain wetlands that are not connected to the river network through a stream channel (i.e., geographical ly isolated wetlands and wetlands that spill into losing streams), connectivity and isolation vary wit hin a watershed and over time, making it difficult to generalize about their connection s to, or isolation from, downstream waters. The literature we reviewed does not provide sufficient information to evaluate the degree of connectivity (absolute or relative) of these non-riparian particular wetlands.
a) Are these conclusions supported by the scientific evidence?
b) Does the report include the most relevant peer-revie wed literature on these topics, including evidence of connectivity and isolation? If not please indicate which references a re missing.
c) Was the reviewed literature cited and summarized cor rectly? If not please indicate where correction or revision is needed.
The conclusion that in the case of non-riparian/non-floodplain w etlands that are not connected to the river network through a stream channel, connectivity and i solation varies within a watershed and over time is well supported by the scientific evidence.
The conclusion that the literature reviewed does not provide s ufficient information to document the connectivity of these systems is correct, but it should be no ted that this is largely because the category includes a mix of wetlands that are truly geographically isol ated and wetlands that are clearly connected to downstream waters. The report should attempt to provide guidance on how to distinguish these two categories (perhaps using soils and other indicators). The r eport distinguishes geographically isolated wetlands as surrounded by uplands but seems to include in this grouping all non-riparian/non-floodplain wetlands that do not outlet to a channel. This concept is i ntroduced on lines 52-54 on page 3 of the Introduction and repeated throughout the report. It is well illustra ted by Figure 3-18 on page 64 in section 3.4.2. Essentially the report places wetlands tha t spill over to a “swale” in the category of geographically isolated wetlands since swales can be “upla nd”. However, it would also include in this category prairie pothole depressions that spill over onto wetla nd flats or slope wetlands rather than to a channel. Wetland depressions that spill over to wetland sys tems (including wetland flats, slope wetlands or hydric swales) should be recognized as a separate catego ry, distinct from wetlands that are completely surrounded by upland and thus more likely to be trul y geographically isolated.

The report provides reasonable coverage of the relevant pee r-reviewed literature on connection and isolation of non-riparian/non-floodplain wetlands to the downst ream waters but does fall short in a few

areas.William G. Crumpton, Ph.D.

A-17 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE The report fails to adequately address the effect of s ubsurface tile drainage on connectivity of these wetlands to downstream waters. The report recognizes that surface drainage and ditching can directly increase connectivity to downstream waters (for exa mple lines 5166-5170 on pages 249- 250 of section 5.8.3.1). The report states that “When pothole s are artificially connected to streams and lakes though drainage, isolation is eliminated and the y become important sources of water and chemicals” (lines 4984-4985 on page 242 in section 5.8.1). However, the report is apparently referring only to surface drainage. Little consideration i s given to the importance of subsurface “tile” drainage which is ubiquitous throughout the Corn Belt a nd many other areas. The report mentions only briefly that “drains fitted at the bottom of po tholes connected to shallow subsurface pipes often discharge to open ditches and streams” (line s 5170-5171 on page 250 of section 5.8.3.1) but is silent on whether this constitutes a direct connection to downstream waters. This is an extremely important issue and the report should clarify the role of subsurface tile drainage (and especially surface intakes to these systems) in providing a connection to downstream waters. Specifically, do surface intakes of subsurface drainage pipe s (“tile drains”) provide a direct connection to downstream waters for what might otherwise b e considered geographically isolated wetlands?

The report in part uses HGM (hydrogeomorphic) wetland class ification and could benefit from a review of the wetland classes in this system. Importan t HGM classes in the Prairie Pothole Region would include for example depressions, flats, and slope wetlands. This classification is useful in that it helps to illustrate connections and surface flow paths in t hese landscapes.
The report should also provide information on the relation ship between soils and wetland classes. Soils can be very useful in determining HGM wetland class, in identifying flow paths and connections, and potentially in distinguishing geographically iso lated wetlands from depressions that are at least intermittently connected to downstream waters through wetland flats or slope wetlands.
The report makes the important point that increased sur face outflow and connectivity is expected in wetter portions of the prairie pothole but extends this analy sis only as far as the Red River Valley and ignores the much wetter and more interconnected wetland s of the Des Moines Lobe (lines 1434- 1437 on page 77 of section 3.4.6 and lines 5138-5143 on page 248 of section5.8.3. 1).William G. Crumpton, Ph.D.

A-18 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE A broader analysis of this pattern for the Prairie Pothole is provided by Johnson et al. ( 2005. Vulnerability of northern prairie wetlands to clima te change. Bioscience 55: 863-873 ). Their models of wetland water regimes suggest that spillo ver to downstream waters is a common occurrence in the wetter portions of the Prairie Po thole Region. For the Des Moines Lobe, spillover was expected in 87 years over a 95 year weather rec ord. Because of the wetter climate, depressional wetlands on the Des Moines Lobe formed as interconn ected systems with significant flow from upslope depressions through wetland flats to downsl ope depressions and from downslope depressions to receiving streams. In this regard, p rairie potholes of the Des Moines Lobe differ from the more isolated basins that are typical of drier parts of the Prairie Pothole region. An analysis of soils illustrates these differences between the mor e interconnected wetlands of the Des Moines Lobe and the more isolated wetlands of the drier portion s of the Prairie Pothole Region.
The literature is for the most part cited and summa rized correctly. However, in several places (line 1 435- 1468 and others), the report incorrectly describes the subregions of the Prairie Pothole Region, essentially ignoring the Des Moines lobe. This is t he southeastern and wettest portion of the Prairie Pothole and as suggested above, its wetlands might be expected to have greater connectivity to downstream waters.William G. Crumpton, Ph.D.

A-19 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE 4. This report concludes that while the influence of a particular stream or wetland on downstream waters might be small, the aggregate contribution by an entire class of streams or wetlands (e.g., all ephemeral streams in the river network, or a cluster of small wetlands) might be substantial.
a) Is this conclusion supported by the scientific evi dence?
b) Does the report include the most relevant peer-revie wed literature on this topic? If not please indicate which references are missing.
c) Was the reviewed literature cited and summarized cor rectly? If not please indicate where correction or revision is needed.
The conclusion that in the aggregate, a class of streams or wetlands might have a substantial effect on downstream waters even though the influence of an individual stream or wetland might be small is clearly supported by the scientific evidence (and by simple c ommon sense).
The report provides sufficient coverage of the relevant peer -reviewed literature on this topic although that literature is by design spread throughout the report i n the treatments of streams, riparian/floodplain wetlands, and non-riparian/non-floodplain wetlands.
The literature relevant to this topic was cited and su mmarized appropriately although its dispersion throughout the document makes it less easily accessible t han that of the other topics.A-21 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE



### Kenneth W. Cummins, Ph.D. Adjunct Professor Department of Fisheries Biology Humbolt State University Arcata, CA

Kenneth W. Cummins, Ph.D. is currently Adjunct Professor, Department of Fisheries Biology, and Senior Scientist, U. S. Geological Survey, California Cooperati ve Fisheries Research Unit - both at Humboldt State University.

Over the past 40 years, Dr. Cummins has been involved in res earch and teaching in the field of freshwater ecology, while on the faculties of Northwestern, Michigan State, Oregon State, Pittsburgh and Maryland Universities. He also held the position of Distinguished Sci entist at the South Florida Water Management District in the Everglades Restoration Program.

“The River Continuum Concept” (RCC), which he co-authored, relates the physical templa te of watershed networks with the biological systems that overlay it, from headwaters to large rivers. After its publication in 1980, topics related to the RCC expanded to include; river- flood plain interactions, localized tributary effects on larger rivers, discontinuities in the RCC i mposed by dams, and changes in freshwater invertebrate community composition along the RCC trajectory. He developed the “ Functional Feeding Group” approach to the analysis of these invertebrate communities. Along with Drs. Richard Merritt and Martin Berg, he is author and editor of “The Aquatic Insects of North America. “ This book, now in its fourth edition, contains tables which allow the categorization of aquatic insect gener a by habitat and functional group. He is widely published in the field of freshwater ecology, some designated as citation classics. Over the last 30 years he has focused on the coupling between riparian vegetation and inve rtebrate and fish populations of streams.

Journals in which Cummins has published:

Ecology; Ecol. Monogr.; Can. J. Fish. Aquat. Sci.; JNABS; BioScience; Limnol. Oceanogr.; Verh. Int. Verein. Limnol.; Freshwat. Biol.; J. Freshwat. Ecol.; Hyd robiologia; Arch. Hydrobiol.; Freshwat. Biol.; Freshwat. Invert.; Oikos; Annals Limnol.; Invert. Biol.; Ame r. Midl. Nat.; Holarctic Ecol.; Environ. Toxicol. Chem.; Organic Geochem.; Annals Ent. Soc. Amer. ; Ann. Rev. Ecol. Systemat.; Ann. Rev. Ent.; Trans. Amer. Microscop. Soc.; Ambio: J. Restor. Ecol.; Florida Sci.Kenneth W. Cummins, Ph.D.

A-23 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE 

### Peer Review Meeting of EPA’s Draft Report: Connectivity of Streams and Wetlands to Downstream Waters – A Review and Synthesis of the Scienti fic Evidence

Comments submitted by Dr. Kenneth W. Cummins

1. This report concludes that all streams regardless of fl ow duration or size, are physically, chemically, and biologically connected to rivers; and these connections, individually or cumulatively, exert a strong influence on the character an d functioning of downstream waters.

a) Are these conclusions supported by the scientific evid ence?
The conclusions are supported by the scientific evidence.

b) Does the report include the most relevant peer-reviewed literature on these topics, including evidence of connectivity and isolation? If not please indicate which references are missing.
By and large the report does include the most relevant peer reviewed literature to address the question. However I have the following comments and recommendations.
Page Line Comment 2 32 ... spiraling... Unlike standing waters where nutrient cycles are closed l oops, the

unidirectional flow of streams creates open cycles in whi ch release of a nutrient is displaced from its uptake site. The open nature of the cyc les needs to be made clear at the outset. (Also, 8, 184; 8, 190; and the entire section 9, 191-206 should include the concept that the cycles are open.) 11 253-60 A major feature of dams is to reverse the seasonal hydr ology of streams and rivers on

which they are constructed. The purpose of most dams is to truncate peak flows in the normal season of high runoff (storage for dry season relea se and use) and to increase flows during these normal low flow seasons. This reversal of normal hydrological patterns has immense implications for life cycles of lo tic organisms. This point should be made here or elsewhere. 15 342-44 Furthermore... isolated. In fact, some ecologists have sugges ted using air-shed,

watershed, and ground-watershed to categorize all the appr oximately definable inputs and cycles with in a region.

23 509-10 Headwater streams are first- and second-order stream s... I feel strongly that

alternatives to this statement should be acknowledged. For e xample, the River Continuum Concept (Vannote et al., 1980, cited 4, 708 times so far) groups first-to third-order streams as those headwater streams in which riparian vegetation dominates the in-stream biology. Most order s one to three ha ve canopy closure sufficient to strongly influence in-stream primary production (designated as P/R <1) and the input of plant litter that is the dominant energy bas e of stream ecosystem function in most headwater streams.Kenneth W. Cummins, Ph.D.

A-24 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE Here, and elsewhere, the point should be driven home tha t stream order is a

geomorphic concept and probably never should be inferred from blu e lines on a map, which can represent anything from first-order to fourth-o rder depending on map scale. In addition, the stream class system of categoriz ing streams by fish-bearing condition (e.g., California Forest Practices Rules, Sect ion 936.4) should be laid to rest. This is not a geomorphic defensible classification and should be permanently discouraged. [“Class I watercourses are defined as fish always or seasonally present onsite, including habitat to sustain fish migration and s pawning. Class II waters are defined as 1) fish always or seasonally present off-site within 1000 feet downstream and/or 2) aquatic habitat for non-fish aquatic species. C lass III watercourses do not have aquatic life present” (This is impossible at all seasons and in all years – e.g., aquatic Diptera, appear within days of flooding of forest ac cess roads) “and are capable of sediment transport to Class I and II waters u nder normal high water flow conditions. (Cummins, K.W. and M.A. Wilzbach. 2005. The inadequacy of the fishbearing criterion for stream management. Aquatic Science s. On line; http://www.birkhauser.ch , pp 1-6). 24 531 ...symmetry ratio... another way is link number, which sums t he total number of

first-order tributaries entering a watershed of a given o rder. Fig. 3-1 shows no firstorder tributaries entering directly into the third-order ma instem which would be quite unusual. Link number is a useful measurer for stream ecol ogists working at the watershed scale because the first-order tributaries are t hose in which the riparian influence on in-stream biological community composition and productivity is maximized 26 559 Fig. 3-3. The diagram’s horizontal bars give no indicati on about the massive

controversy about the width of riparian areas. This point is the major element of all forest practice rules, including the sentinel Northwest Fo rest Plan, that define the width in terms of tree height in the riparian area. The point that need s to be acknowledged (driven home), is that stream ecologists, fisheri es managers, and forestry managers all have different concepts (or biases) about the definition of the width. For example, stream ecologists may focus on the widt h necessary to provide the width that supplies plant litter that constitutes the pr imary energy source of headwater stream ecosystems, fisheries managers are conc erned with the width necessary to insure the input of large wood which is the mai nstay of fish habitat in streams and rivers in general, and forestry managers are concerned with how much width will be excluded from harvest by almost all forest practices rules. So, for scientific, Endangered Species Act, and economic reasons def ining the width, or the criteria for defining the width of the riparian zone is far from a trivial matter. At least replace the end bars on the riparian widths in Fig. 3-3 wit h a dashed line at the ends. The figure caption should explain that the dash lines indica te that the boundary of the riparian zone depends upon the function being considered (e.g., Gregory et al., 1991).Kenneth W. Cummins, Ph.D.

A-25 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE 51 1000 Figure 3-14). Also, dissolved organic matter (DOM) forms complexes with divalent

cations, primarily Ca, converting DOM to fine particulate organic matter (FPOM, particle size < 1mm) and is taken up directly by benthic bac teria. This significantly delays the export of organic matter down river. DOM almos t universally accounts for 50% of all the organic matter in transport in all order s treams (Vannote et al., 1980 and the Minshall et al., River Continuum publications). T his retention of FPOM, rather than loss as DOM, has major consequences for st ream and river invertebrates and is likely a major factor in the productivity of har d water (calcium rich) streams. 80 1484 Swanson et al. (1987) suggest that short recurrence inte rvals involve flows too small

to cause significant changes in stream channel geomorphology, a nd very long recurrence intervals cause very major alterations in ch annel form, but the intermediate recurrence intervals are the events that have the major effects in shaping the current condition of most channels.[Swanson, F. J., L. E. Benda, S. H . Duncan, G. E. Grant, W. E. Megahan, L. M. Reid, and R. R. Zimmer. 1987. Mass failures and other processes of sediment production in Pacific Northwest fore st landscapes. Pp. 91-138 in : Salo, E. O. and T. W. Cundy. (eds.). Streamside mana gement: forestry and fisheries interactions. Institute of Forest Resources, Univ. Washington, Seattle. (If the NRC publication is cited, this one should be eligible as w ell; it was reviewed by outsiders.)] 108 2106 Cite Cushing et al. (eds.), 2006. This 817 page volume includes chapters by

worldwide authors on streams and rivers of North America, Central and south America, Europe, Africa, Asia, Australia and New Zeala nd, and Oceana. The editors charged the authors with using data from streams and rivers in their respective regions and comparing it with the River Continuum Concept (Vannote et al., 1980). The comparisons are about linkages (connectivity) between headwater streams and large rivers on a world wide scale. The introduction by the edito rs presents an overview of stream ecosystems. The River Continuum Conceptual Model (Vanno te et al., 1980) is reproduced in the Introduction. This is the model that relat es stream/river ecological structure and function to the position along the downstream tr ajectory. (Cushing, C. E., K. W. Cummins, and G. W. Minshall. 2006. River and str eam ecosystems of the world. Univ. California Press, Berkeley 817 p.) 110 2145 ...108 m for whole leaves... This compares to the 100 m in Cummins e t al. (1989)

and not to the 1000 m cited in this report. 112 2197 ...snow melt. Approximately 50% of transported carbon was D OC in all streams

(orders 1-8) covered in the River Continuum studies (Vannote et al., 1980, Minshall et al., 1983, 1992). 112 2206 ...river network. An important point here is that anaerobi c storage of CPOM, e.g.,

leaf litter, greatly delays breakdown of CPOM to FPOM i n the absence of hyphomeycete fungi and shredders, both of which are obligate aerobes (Cummins et al., 1980. [Cummins, K.W., G.L. Spengler, G.M. Ward, R.M. Speaker, R.W. Ovink,Kenneth W. Cummins, Ph.D.

A-26 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE DC Mahan, and R.L. Mattingly. 1980. Processing of confined a nd naturally entrained leaf litter in a woodland stream ecosystem. Limnol. Oceano gr. 25:952-957.] 120 2382 Wilzbach and Cummins (1989 ) demonstrated a higher % morta lity among drifting

individuals than their benthic counterparts. This raises t he possibility that a significant amount of invertebrate stream drift is destined to have no impact on downstream colonization of invertebrates, with the primary effect being t he contribution being to the downstream detrital suspended load. (Wilzbach, M. A. and K. W. Cummins. 1989. An assessment of short-term depletion of stream mac robenthos by drift. Hydrobiologia 185: 29-39.) 146 2970 ...gatherers, the dominant group... the term is defined, but as in the case of shredders (which was not defined or referenced when used) no citation is given. There are a great many that could be used, e.g., Cummins 1974, Cummins a nd Klug 1979. [Cummins, K.W. 1974. Structure and function of stream eco systems. BioScience 24: 631-641; Cummins, K.W. and M.J. Klug. 1979. Feeding ecology of str eam invertebrates. Ann. Rev. Ecol. Syst. 10:147-172; the designations are also part of the River Continuum Concept.] 148 3002 ...reaches 500 and 1,000 m upstream. Distance traveled by the ma jority of introduced leaf litter in a forested second-order stream by reporte d to be about 100 m by Cummins et al. (1989). [Travel distance of leaf litter w as reported from the time the litter is wetted. Senescent Ginkgo leaves were used in t hese experiments; they are bright yellow and remain so for several weeks because they are very resistant to biological processing. Also, the leaf shape is unlike any of t he native riparian tree species in eastern headwater streams.] Attached is a figure that might be of interest to some p eople at the meeting. I make no suggestion whatsoever that this Figure should be any part of the repor t. It is merely a “snap shot” offered in support of the argument that I did make in the report about incl uding more detail on one of the sentinel features of connectivity between riparian vegetation and structure, function and productivity of invertebrate populations in headwater streams (which I would define as fi rst- to third-order). The photograph is not unique; this sort of picture could be taken of leaf lit ter from any stream in the world during any season when riparian plant litter is available in streams (inc luding intermittent channels). I have such pictures from streams in southern and northern California, Oregon, Ne w Mexico, Yellowstone Park (Wyoming and Montana), Idaho, Michigan, Pennsylvania, Maryland, Fl orida, Sweden, Denmark, Italy, Australia, New Zealand, Brazil, and Guinea West Africa.Kenneth W. Cummins, Ph.D.

A-27 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE Fig. A. Conditioned red alder leaf eaten by caddisf ly (Trichoptera) larvae. Note: better conditioned ( higher aquatic hyphomycete fungal biomass) soft tissues ea ten in preference to the poorly conditioned midrib and major veins which are high in lignin. (Cummins et a l., 1989).
Just for background information. A companion to the comment at page 146, Line 2970, Response to Techni cal Charge Question 1.

So, as I argued in one of my comments in Response to Cha rge question 1, this world wide and highly predictable connection between riparian vegetation and in – stre am biology is worthy of more than the undefined use of the term “shredders” which occurs at a single place in the report. There are over 1,000 references in the literature that address this example of connectivity.

c) Was the reviewed literature cited and summarized correc tly? If not please indicate where correction or revision is needed.

The Literature that was cited was summarized correctl y.

2. This report concludes that open water and wetlands and riparian areas and floodplains of streams and rivers are physically, chemically, and biologically connect ed with the river net work, and that their functions exert a strong influence on the char acter and functioning of downstream waters.

a) Are these conclusions supported by the scientific evid ence?
The conclusions are supported by the scientific evidence.Kenneth W. Cummins, Ph.D.

A-28 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE b) Does the report include the most relevant peer-reviewed literature on these topics, including evidence of connectivity and isolation? If not please indicate which references are missing.
By and large the report does include the most relevant peer reviewed literature to address the question. However I have the following comments and recommendations.

Page Line Comment 7 161 ...rivers. At some point, perhaps here, cases in which headwa ter streams are not the

initial source of river networks should be flagged. For exam ple, the Yellowstone River (one of the longest and largest un-dammed rivers in Nort h America) originates from Yellowstone Lake. The lake itself is fed by numerous small tributaries which are not episodic connections. This natural configuration conforms to essentially all human-constructed reservoirs in North America. 175 3573 ...outside edges of riparian areas... See comment 26, 559 (Fig. 3- 3). This implies the

width of riparian areas has been defined (as argued at 2 6, 559, there is little agreement about this, because the width is dependent upon the fu nction being considered or the management objectives dependent upon the width as define by regulations. For example, foresters interested in timb er harvest will argue for the smallest width possible while fisheries managers will ar gue for a width sufficient to provide recruitment of LWD. 177 3615 ...such as black willow... As discussed at 74, 1363, the physical bank stabilization

characteristics if black willow need to be balance agai nst the potential disruptive effects on the aquatic ecosystem involved, e.g., stream o r wetland. A very important point about connectivity between the riparian zone and the adjace nt aquatic system and, therefore, the connectivity downstream is that the plan t species composition of the riparian has a very significant impact on the timing a nd nature of these downstream contributions. (e.g., Cummins et al., 1989). 184 3771-72 Allochthonous inputs...food webs... (reviewed in Tank et al., 2010). T his could use

some other review references (e.g., Cummins 1974, Vannote et al. 1980, Cummins 2002) and many others). [Cummins, K. W. 2002. Riparian-stream linkage paradigm. Verh. Verein. Limnol. 28: 49-58.] 187 3842-44 Thus, lateral... river systems. Here or elsewhere cite Junk et al., 1989. Most stream ecologists would cite this paper as one of the major additions to the River Continuum Concept. [Junk, W. J., P. B. Bayley, and R. E. Sparks. 1989. Th e Flood Pulse Concept 9n river

floodplain systems. Pp 110-127 in : Dodge, D. P. Proceedings of the international large river symposium. Can. Spec. Publ. fih. Aquat. Sci. 106 .]
189 3881-82 See also notes about black willow (74, 1363; 177, 3771-72.Kenneth W. Cummins, Ph.D.

A-29 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE c) Was the reviewed literature cited and summarized correc tly? If not please indicate where correction or revision is needed.
Literature was cited and summarized correctly. (Except see note at 184, 3771-72)

3. This report concludes that for non-riparian/non-flood plain wetlands that are not connected to the river network through a stream channel (i.e., geographical ly isolated wetlands and wetlands that spill into losing streams), connectivity and isolation vary wit hin a watershed and over time, making it difficult to generalize about their connection s to, or isolation from, downstream rivers. The literature we reviewed does not provide sufficient information to evaluate the degree of connectivity (absolute or relative) of these non-riparian particular wetlands.

a) Are these conclusions supported by the scientific evid ence?
The conclusions are supported by the scientific evidence.
In general they are supported by the literature cited. Howeve r, I find this section very hard to evaluate objectively because the reason for separating out NRCWs as a class of connectivity is not clear. As noted in the underlined portion of the question above, there is no reason for this conceptual category.
There was a lot of discussion at the Committee Meeting a bout a reorganization of the information that was presented in the Document. I think the general thrust o f the recommendation would improve the Document and not require much, if anything, in the way of new informa tion.
The organization would not be levels of connectivity but rather functional classes of connectivity: hydrologic, physical (geomorphic), chemical (nutrients/ pollut ants), and biological (ecological). Within each of these classes there would be continua of connectivit y described as probabilities. Namely spatial and temporal probabilities of degree of connectedness. As wa s suggested, a conceptual model could be presented for each. For example, ephemeral streams have a low probability of connectivity on any given day in any given year, whereas perennial streams have a near 100% probability of connectivity along the same time continuum. The more spatially separated stream s and wetlands of various types are, the lower probability they will exhibit high connectivity on any time scal e.
This more functional approach would provide, I believe, a be tter frame work for handling the problem of conceptual models for isolated (surrounded by uplands) wetl ands and allows for the concept that there are no examples of biological isolation, because mig rations will always bridge hydrologic, physical, and chemical isolation.

b) Does the report include the most relevant peer-reviewed literature on these topics, including evidence of connectivity and isolation? If not please indicate which references are missing.
This report includes the most relevant peer-reviewed liter ature on those topics, including evidence of connectivity and isolation as presented. However, if a diff erent organization of the report is adopted, as discussed above, a reorganization of the references cited wo uld beKenneth W. Cummins, Ph.D.

A-30 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE c) Was the reviewed literature cited and summarized correc tly? If not please indicate where correction or revision is needed.
Literature was cited and summarized correctly. Yes.

4. This report concludes that while the influence of a particular stream or wetland on downstream waters might be small, the aggregate contribution of an entire class of streams or wetlands (e.g.; all ephemeral streams in the river network, or a cluster of small wetlands) might be substantial.

a) Is this conclusion supported by the scientific eviden ce?
The conclusions are supported by the scientific evidence.

b) Does the report include the most relevant peer-reviewed literature on this topic? If not please indicate which references are missing.
This report includes the most relevant peer-reviewed liter ature on those topics, including evidence of connectivity and isolation. This question has already been addressed in detail under the other charge questions. There seems little reason to simply transfe r those comments (especially Charge Question 1) to this spot. I find the charge question redundant. Whereas the first three charge questions more or less apply to sections 3, 5 (5.1-5.3) and 5.4 of the report, respec tively. There is no separate section that corresponds to Charge Question 4. If one uses the find option in Word and inserts intermediate or ephemeral streams or small wetlands in the search, one o r both of these appear in essentially every subsection of the entire report. In reading the report I c oncluded that these entries were accompanied by appropriate citations. The comments provided under Question 3 apply here as well. If the Report was organized functionally, this section would be subsumed under each of the functional conceptual models.

c) Was the reviewed literature cited and summarized correc tly? If not please indicate where correction or revision is needed.

The reviewed literature was cited and summarized cor rectly, or relevant comments were covered under the first three Charge Questions (e.g., comments about ad aptations by invertebrate life cycles to accommodate periodic drying, in which the annual predictable se asonal flows of intermittent streams have more taxa adapted to the condition than in ephemeral st reams, in which annual flows can only be described in terms of probabilities).



### Additional Comments (via email)
There was a lot of discussion at the meeting about a r eorganization of the information that was presented in the Document. I think the general thrust of th e recommendation would improve the Document and not require much if anything in the way of ne w information.
The organization would not be levels of connectivity but rather functional classes of connectivity: hydrologic, physical (geomorphic), chemical (nutrients/ pollut ants), and biological (ecological). Within each

of these classes there would be continua of connectivit y described as probabilities.Kenneth W. Cummins, Ph.D.

A-31 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE 

### Namely spatial and temporal probabilities of degree of con nectedness. For example, ephemeral streams have a low probability of connectivity on any give n day in any given year, whereas perennial streams have a near 100% probability of connectivity along the same time continuum. The more spatially separated streams and wetlands of var ious types are, the lower probability they will exhibit high connectivity on any time scale.
This more functional approach gives, I believe, a better frame work for handling the problem of conceptual models for isolated (surrounded by uplands) wetlan ds and allows for the concept that there are no examples of biological isolation, because migrations will always bridge hydrologic, physical, and chemical isolation.

Other Additional Comments

Page Line(s) Comments 2 28 ... plants, microorganisms, and... 4 81 replace lack with back 8 176 ...series of complex physical, chemical, and biological alte rations...

10 223 ... lakes and lakes and reservoirs that form nodes in rive r systems. 12 261-2 ...of sediment and organic matter... before they enter... 13 306-8 The impacts ... habitat, and ecology. The concept discusse d in 11, 253-60 also applies

here. 15 334 ...and invertebrates and vertebrates between...( fish and amp hibian eggs have been

isolated from migratory ducks feet)

17 398 ... the term... Then why use it? 19 424 ...oxbow lakes, “node” and pater noster lakes 20 443 ... scientific community... not those ignoring non-peer revie wed literature. Also, the

statement about peer reviewed literature only being used is not true – p 311, 7055, National Research Council 2002 reference was not peer revie wed literature. 21 477-8 Again, I would argue that this report has a more tho rough and unbiased literature

review than most “peer reviewed” papers.
25 539 First Vannote et al., 1980 citation. Introduce River Conti nuum Concept phrase used

therein. 25 546 Fig. 3-2. You need a magnifying glass to distinguish epheme ral streams.Kenneth W. Cummins, Ph.D.

A-32 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE 27 583 Use an acronym for riparian/floodplain wetlands (R/FWs) or spell out non-riparian and

channel origin floodplains (NRCWs). Use acronym for both o r spell out both throughout the document.
28 661-2 See comment at 20, 443 above. 33 689-90 ...and references therein). This is a useful phrase to a dd where warranted because it

indicates at least a partial review of the subject is in cluded; could be useful other places in the report. 34 699 ...precipitation and are not seasonally controlled. 34 715 ...Hunter et al., 2005) and have major consequences for the dis tribution and seasonality

of stream biota. 39 774 Fig. 3-10 has a much better representation of ephemeral streams than Fig. 3-2 (25, 546).

42 826 Delete has

. 48 929-31 This is another argument for using link number. (see 24, 531; introduced at 122, 531 as useful but probably should be introduced here.
50 964 Vannote et al., 1980 should also be cited here. 51 1001 ...be eaten by other invertebrates and by aquatic vertebrates , especially juvenile fish

that eventually ...

51 1001 Delete further ; ambiguous. 52 1006 Fig. 3-14. This is an interesting take on the original Va nnote et al., 1980 conceptual

model. Perhaps a citation or two would be warranted here

. 53 1017 ...basin can be transported back to a river only by terrest rial (over land) movement and

not by a hydrological pathway. 54 1047-8 ...100 year floodplain. Introduce the concept of recurrence int ervals (it appears later in

the report. 56 1104 A statement is warranted about the “man-made paving” of essentially all urban

watersheds in the U.S. resulting in quick flow as the rul e. 59 1139 The Metolius River emerges and immediately assumes the ec ological characteristics of

a fourth-order river, with no headwater biological inputs and constant year around flow and temperature that completely alters life history pat terns typical for streams of the region. (Fig. 3-15E; 57, 1105.) 61 1180 Define stream power (math formula) here or elsewhere. 63 1215 Fig. 3-17. Perhaps point out that C fits the pattern of q uick flow for “paved” urban stream watersheds.Kenneth W. Cummins, Ph.D.

A-33 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE 65 1240-42 See comment for 11, 253-60. 66. 162 Fig. 3-19. The use of link number can be seen in the fi gure. The trellis watershed is a

third-order with a link number of 13 and the fourth-order dendritic watershed has a link number of 14. Riparian-dependent headwater ecological effects would be greater in the third order watershed.
73 1344 ...Eikeland 1988, add Rader, 1997, ... [Rader, R. B. 1997. A functional classificat ion

of the drift: traits that influence invertebrate availabi lity to salmonids. Can. J. Fish. Aquat. Sci. 54:1211-1234.] 74 1363 ...movement and alter ecosystem function as in the case i n which stream bank

stabilization is accomplished by planting non-native willow t o replace various species of alder. Alder (nitrogen fixers) litter is utilized at 5 to 10 times the rate of willow in headwater streams. 74 1374 ...al. 2011) and form a discontinuity in the normal stream -order related progression in

stream ecosystem structure and function. (Ward, J. V. and J. A. Stanford. (eds.). 1982. The ecology of regulated streams. Plenum, N. Y. 398 p. 81 1151 ...and ephemeral streams, even though these watershed repre sent only ??% (small) of

the land area of the United States. 82 1517-18 Another argument for link number inventory. 82 1519-30 Make it clear that stream order is a geomorphic cl assification and not a blue line map criterion. If the tenets of connectivity in this report ar e to be honored, development of new watershed concepts and advancement in research and land management plans must not be blue line map based. 83 1551-53 As per the statement on 82, 1526 (...Despite this underestimat ion...), this raises

important questions about the data. 85 1604-06 Again, this might be a useful approximation, but it shows t hat, in general, map blue line

analysis cannot be used to clarify the actual physical, che mical, and, especially biological, importance of geomorphic first-order channels in a watershed. 85 1608 ...and river flows, as long as headwater streams are define d as second-order channels.

87 1630 ...return interval... First mention of recurrence interval. Here, or elsewhere it should be

defined (calculation method) and its utility discussed. 91 1706 ...Suspended sediment... The question of suspended fine particulate o rganic particles

should be acknowledged. FPOM is a significant contributor to turbidity (first to be entrained on the rising limb of the hydrograph and the last to settle out on the falling limb) and biologically by far the most important component of the suspended load. 93 1763 ...inorganic + organic... First mention of the organic component; should appear earlier.Kenneth W. Cummins, Ph.D.

A-34 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE 94 1796 LWD in stream of the western Cascades in Oregon measur ed to have been in place for

over 100 years. 96 1838 ...important habitat for aquatic life... Not just habitat; LWD has a major role as a long

term source of slowly processed DOM and FPOM that is uti lized by stream microbes and invertebrates. 97 1858 ...diel changes typical of intermediate sized streams... a nd rivers. Larger daily

temperature excursions in mid-sized rivers is one of two reasons proposed (Vannote et al., 1980; orders 4-6) for the usually maximized biological diversi ty of these rivers. (Aquatic organisms have differing temperature optima, and a wide daily range of temperature excursion provides more species to spend at le ast part of every 24 hours in their optimum range.) 100 1915 ...chemical linkages through open cycle spiraling. 107 2088 ...terrestrial plant litter... (in addition to leaf litter, other riparian plant par ts can

dominate seasonally, e.g., catkins.
108 2106 Cite Petersen et al., 1989. [Petersen, R.C., K.W. Cumm ins, and G.M. Ward. 1989.

Microbial and animal processing of detritus in a woodland s tream. Ecol. Monogr. 59:21-39.
109 2113 In this reference (and Vannote et al., 1980, and most of the other related ones I know

of) headwater streams would be orders 1 – 3.

112 2187 ...... downstream (Petersen et al., 1989, Gomi et al., ... 112 2198 ...et al., 2007) or in spring when other plant parts are shed , e.g., bud scales, flowers,

catkins). 113 2219 ...et al., 2005). Diatoms continue to photosynthesize and i nvertebrates continue to feed

and grow at 0 ̊C. In fact, the majority of shredders acco mplish all of their growth in the winter and remain inactive all summer in streams in forested areas (Cummins et al., 1989). 114 2235 The main point of the note here is that it should be a cknowledged that connectivity can

be on a diurnal scale as well as longer time periods. Wee kly grab samples for DOC at 10 locations throughout the Augusta Creek were taken in southw estern Michigan for two years. Locations were sampled in sequence each we ek from 1 through 10 in the same sequential order. The data showed significant differ ences in DOC concentrations between the sites. When samples were taken every 2 hours over 24 hours at 1 site, the difference in the values were equal to the difference in the values between the 10 sites over 2 years. What appeared to be differences between sites over the 2 years were due entirely to the time of day when the samples were taken which was essentially the same each week because of the regular sampling schedule.Kenneth W. Cummins, Ph.D.

A-35 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE 119 2374 Many invertebrates have life cycles that “expect” (are adapted to) dry and/or wet and

/or hot or cold periods for the completion of their life cycles. Some may even require these periods. 120 2380 ......drifting insects (Rader 1997, Nakano... 120 2388 ...et al., 2006) and diel invertebrate behavioral patterns t hat are independent of flow

(Rader 1997). 122 2439 ...higher prey and lower predator densities...

129 2605-06 Most often the only shrubs and trees in grassland biomes are along the water courses.

This has significant implications for the in-stream biology (e.g., shading, litter inputs). 135 2737-38 flooding and drying..., spur successional sequences. Flooding is just as important in

forested streams in resetting algal succession. 137 2765 ...surprisingly rapid. Why surprising? This is merely an exam ple of the adaptation one would expect. 138 2808 ...was once limited by floods,... Is there post glacial evidence for this? Or, is “once ”

merely before agriculture cut the prairie? 146 2470 The functional feeding group (FFG) for categorizing fre shwater invertebrates (e.g.,

Cummins and Klug 1979, Merritt et al., 2008) should be used (and defined) throughout the Report. There is a large literature extending over 30 yea rs that utilizes this functional categorization on a world- wide basis (e.g., Cus hing et al., 2002). The FFG meshes well with the concepts of connectivity. Arguably, the best indicator of normal (statistically probable) linkage (coupling)

between riparian vegetation and stream biota is the presence of invertebrate shredders (e.g., Cummins and Klug 1979, Grubbs and Cummins 1996, Merritt e t al., 2008). The sequence is well known and has been demonstrated around the wo rld (Cushing et al., 2006): 1) Riparian leaf is entrained in freshwater system; 2) leaf leaches DOM (up to 40 % of dry mass); 3)Leaf rich in carbon, lower in nitrogen , colonized by hyphomeycete fungi (and bacteria), leaf species vary significantly in t he length of time required for hyphomycetes to develop hyphal growth in leaf matrix – termed conditioning; 4) Shredder invertebrates seek out and feed on leaf or parts of leaf highest in hyphomeycete biomass; 5) shredder feeding produces large amounts of FPOM (< 1 mm particle size feces and leaf fragments); 6) shredder fee ding and temperature (number of degree days) accurately predict the period required to pr ocess a leaf from a given species of riparian plant (e.g., Petersen and Cummins 1974)

. [Grubbs, S.A. and K.W. Cummins. 1996. Linkages between ripar ian forest composition

and shredder voltinism. Arch. Hydrobiol. 137:39-58. Merritt. R. W, K. W. Cummins, and M. B. Berg. (eds.). 2008. An introduction to the aquatic insects of North America (4 th edition). Kendall/Hunt, Dubuque, IA 1158p. . Petersen, R.C. a nd K.W. Cummins. 1974. Leaf processing in a woodland stream. Freshwat. Biol. 4: 343-368.]Kenneth W. Cummins, Ph.D.

A-36 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE 146 2965 ...richness... Is this species richness? It would be more l ikely density. 146 2966-67 This is a basic tenet of the River Continuum Concept. 147 2977 ...filterers (macroinvertebrates ...suspended FPOM)... Citation? S ee 146, 2970. 148 3016-17 Again, it should be made clear that “richness” is t axa richness. 161 3270 [A note. This section makes one wonder if the organization o f the report should have

been by ecoregion, with the four aquatic system types as subheadings under each because the discussion of each of the four is so driven by eco region setting. 177 3622 ...length of the riparian area... This is ambiguous? Portion of the stream length that is bordered by riparian vegetation, or should this actually be wid th? 178 3650 ...productivity of vascular plants and algae... 179 3661 stream shading...be beneficial to fish and biota... Cooler temperatures beneficial to

(non-fish) biota? According to Q10 relationships, cooler temp eratures would slow production of invertebrates. How would the slowing of production of potential prey for fish be beneficial for fish? 179 3663 ...is used... used by managers? 181 3707 This sentence is too vague. What is being managed? The forest, fish, bank erosion, etc.? 181 3719 This may not be the place to address this, but many ripari an corridors are dominated by

shrubby or tree (red) alders that are nitrogen fixers and constitute a major source of nitrogen.A-37 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE



### Walter K. Dodds, Ph.D. University Distinguished Professor Division of Biology Kansas State University Manhattan, KS

Walter Dodds, University Distinguished Professor in Biology at Kansas State University (KSU), is recognized nationally and internationally as one of the l eading researchers on aquatic ecology and is known for his work on river and stream ecosystems and how human influences affect water quality and biological integrity. His research has focused on whole system rat es of N flux, scaling N transformation and flux rates in stream reaches to entire watersheds, and modeling the effects of land use on downstream transport of excess N. He leads the aquatic ecology research group for the Konza Prairie Long-Term Ecological Research program which has developed new conceptual models of grassland stream ecosystem function.

As a lead principle investigator at KSU, Dodds has recei ved more than $5 million in extramural funding from various agencies including the National Science Founda tion, U.S. Environmental Protection Agency and Kansas Department of Health and Environment. In 1986 Dodds obtained a Ph.D. from the University of Oregon. He received an NSF Postdoctoral Fellowship at M ontana State University in 1988 and joined the KState Division of Biology faculty in 1990. He was hosted on sabb atical at the National Institute of Water and Atmospheric Research in Christchurch New Zealand in 1996. W ith over 125 refereed publications to his credit, Walter Dodds is the author of three books in his dis cipline. His textbook Freshwater Ecology: Concepts and Environmental Applications is one of the defining te xtbooks in the field.Walter K. Dodds, Ph.D.

A-39 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE 

### Peer Review Meeting of EPA’s Draft Report: Connectivity of Streams and Wetlands to Downstream Waters – A Review and Synthesis of the Scienti fic Evidence

Comments submitted by Dr. Walter K. Dodds

This report is generally very well written. It clearly makes the case for connectivity of both streams and wetlands to downstream waters based on many published sources of information. I particularly like the framework of source, sink, refuge, transformation and la g to identify key functions. This approach really allows the issue at hand to be very clearly explored. How ever, this framework is not really clearly delineated throughout the document, and I think the document would be stre ngthened by some slight reorganization along these lines.

In a broad sense, the document indicates that the burden of proof should be on those claiming a stream or a wetland is not connected to downstream waters. The verbiage on lines 5617-5623 is a good example of this concept and potential problems with assuming lack of connecti vity.

1. This report concludes that all streams, regardless of f low duration or size, are physically, chemically, and biologically connected to rivers; and these connections, individually or cumulatively, exert a strong influence on the character an d functioning of downstream waters.

a) Are these conclusions supported by the scientific evidence?
For the most part, these conclusions are supported by the s cientific evidence. There are a very few cases, where streams flow from wet areas (e.g., mountains) int o dry areas (e.g., deserts), where streams might not connect to any downstream waters. However, these sites are the exception, not the rule.

b) Does the report include the most relevant peer-revie wed literature on these topics, including evidence of connectivity and isolation? If not please indicate which references are missing.
This report is well referenced. There are so many refe rences on this subject, that it would be impossible to include them all. The document however, does cite plenty of references that clearly illustrate the main points of the report.

c) Was the reviewed literature cited and summarized cor rectly? If not please indicate where correction or revision is needed.
Yes, the literature was reviewed and cited correctly. O ne minor addition could be that there is one reference that is cited, Dodds and Oakes 2006 that indicate s that intermittent streams are connected chemically to larger streams and rivers even during times of the year when the streams are not flowing. This point is not mentioned but is very important to the issue of connectivity.
I found the illustrative materials in this section quite useful and well done. However, I would like to see the figures such as 3-6 include diagrams of losing stream re aches as well, although figure 3-13 helps. Also a figure with a longitudinal cross section indicating hyp orheic flow, and how such flow can connect isolated pools during dry periods could also be use ful. Finally, Table 3-1 is a bit confusing as itWalter K. Dodds, Ph.D.

A-40 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE looks like everything flows into everything else through the r iver.. I would just lose the multiple italicized words in the first column that say “River”, or space out the individual rows further to make it clear that each row is not linking to the next. I think figur e 3-14 is somewhat misleading as it ignores cycling through inorganic forms.
Line 1031, these streams flow during and immediately following pr ecipitation.
A clearer discussion of when increased connectivity can be ba d (e.g., introduced species) might be useful. The information was in the document, but buried. (e.g ., at line 1408).
Line 1772, confluences are not “much like dams”, they can ch ange longitudinal patterns, but much less severely and in very different ways from dams.

Line 1793. In the Flint Hills of Kansas, wood does not accumul ate in small streams, and such streams are an important source of large wood to downstream river s. This wood is very important habitat as well as a geomorphologic force in rivers. This statement might ne ed to be qualified a bit.
Line 2495, might want to discuss the Falke and Gido 2006 (in refere nces) work here on reservoirs disconnecting small streams from each other.
Line 2560. This could be stated more strongly. The evidence une quivocally demonstrates connectivity between streams and downstream rivers.

Line 2589 Work of Alexander et al. (2000) and Mulholland et al. (2008) , Woolheim et al. (2008) both explicitly examine movement of materials along river network. This reference is also important Helton, A.M., Poole, G.C., Meyer, J.L., Wollheim, W.M., Peters on, B.J., Mulholland, P.J., Bernhardt, E.S., Stanford, J.A., Arango, C. & Ashkenas, L.R. (2010) Thinking outside the channel: modeling nitrogen cycling in networked river ecosystems. Frontiers in Ecology and the Environment, 9, 229-238.

Line 2718. The fact that nutrients are elevated in most e coregions, and these are generally related to non-point source land use characteristics, is highly indicat ive of stream connection. Dodds, W.K. & Oakes, R.M. (2004) A technique for establishing reference nut rient concentrations across watersheds affected by humans. Limnology and Oceanography Methods, 2, 333-341.
Line 2750, these are still net heterotrophic, so they are der ived to a lesser degree than forested areas.
Line 3059, this pattern was also probably driven by bass in the impoundments
Figure 4-9 the title is wrongWalter K. Dodds, Ph.D.

A-41 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE 2. This report concludes that open water and wetlands in riparian areas and floodplains of streams and rivers are physically, chemically, and biologically connect ed with the river network, and that their functions exert a strong influence on the char acter and functioning of downstream waters.

a) Are these conclusions supported by the scientific evidence?
Yes, these conclusions are supported

b) Does the report include the most relevant peer-revie wed literature on these topics, including evidence of connectivity and isolation? If not please indicate which references are missing.

Yes, there is much current and relevant literature cit ed.

c) Was the reviewed literature cited and summarized cor rectly? If not please indicate where correction or revision is needed.
The only major issue I have with this section is not so clearly separating literature on riparian areas that are not technically wetlands from those that are. I under stand that the authors of this document did not want to leave out riparian areas completely because it i s clear that ANY riparian area is connected to the stream it abuts. However, there needs to be clearer separat ion of these. Perhaps a specific section on riparian areas generally, then a second on riparian wetla nd areas.
Table 5-2, not only is considering a stream without riparian influence limiting, it will give incorrect results. Also in this table, water storage needs to be mentioned
Line 4496, might also want to include work by David Galat
Galat, D.L., Fredrickson, L.H., Humburg, D.D., Bataille , K.J., Bodie, J.R., Dohrenwend, J., Gelwicks, G.T., Havel, J.E., Helmers, D.L., Hooker, J.B., Jones, J.R., Knowlton, M.F., J. Kubisiak, J.M., Mccolpin, A.C., Renken, R.B. & Semlitsch, R.D. (1998) Floo ding to restore connectivity of regulated, large-river wetlands. Bioscience, 48, 721-733.
Galat, D.L. & Lopkin, R. (2000) Restoring ecological integri ty of great rivers: historical hydrographs aid in defining reference conditions for the Missouri River. Hydrobiologia, 422/423, 29-48.
Galat, D.L. & Zweimüller, I. (2001) Conserving large-river fishes: is the highway analogy an appropriate paradigm? Journal of the North American Benthological Society, 20, 266-279.
I am surprised there is not more on the Kissimmee restor ation as wetland connectivity was essential to this project. The Dahm, C.N., Cummins, K.W., Valett, H .M. & Coleman, R.L. (1995) An ecosystem view of the restoration of the Kissimmee River. Restoration Ecology, 3, 225-238.Walter K. Dodds, Ph.D.

A-42 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE 3. This report concludes that for non-riparian/non-flood plain wetlands that are not connected to the river network through a stream channel (i.e., geographical ly isolated wetlands and wetlands that spill into losing streams), connectivity and isolation vary wit hin a watershed and over time, making it difficult to generalize about their connection s to, or isolation from, downstream waters. The literature we reviewed does not provide sufficient information to evaluate the degree of connectivity (absolute or relative) of these non-riparian particular wetlands.

a) Are these conclusions supported by the scientific evidence?
Yes they are. However, the authors could have made a stronger statement here. One way to look at the issue is that if a wetland is not connected at all to ot her waters, then the only output of water must be evaporation. If this is the case then wetlands must be sali ne because salts will collect. As many if not most of these wetlands are not highly saline, there is str ong indication that most wetlands are indeed connected to downstream waters either directly or through g roundwater.

b) Does the report include the most relevant peer-revie wed literature on these topics, including evidence of connectivity and isolation? If not please indicate which references are missing.
Yes, this is made very clear. Isolation is certainly a n issue mostly with the biological data, and they cover this well.
There has been a good amount of work on groundwater connection s in the Highland Lake District of Wisconsin, and these connections include wetlands. One refe rence on this might be :Hunt, R.J., Strand, M. & Walker, J.F. (2006) Measuring groundwater-surface water interaction and its effect on wetland stream benthic productivity, Trout Lake watershed, northern Wisconsin, USA. Journal of Hydrology, 320, 370-384.
There is a huge amount of work on hydrologic and chemical connec tion in the Everglades. This should probably be covered a bit better here.
Line 4835. Why all of a sudden a section on human alterations here, where there are other human alterations throughout? This section is just a bit inconsis tent with the rest of the report.

c) Was the reviewed literature cited and summarized cor rectly? If not please indicate where correction or revision is needed.
Yes, this is cited and summarized correctly.

Line 5177 the word detrimental is loaded, if it is a natura l accumulation, then not quite sure how it is viewed as detrimental.
I am not really clear on how vernal pools are substantially different than the prairie potholes for the purposes of this document. The criteria on 5345 could apply to many of them.Walter K. Dodds, Ph.D.

A-43 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE 4. This report concludes that while the influence of a particular stream or wetland on downstream waters might be small, the aggregate contribution by an entire class of streams or wetlands (e.g., all ephemeral streams in the river network, or a cluster of small wetlands) might be substantial.

a) Is this conclusion supported by the scientific evi dence?
Yes, this is a very important point of this document. This point is actually true for any non-point pollution source, and the entire field of watershed manage ment and TMDL’s is based on this idea. Once the systems are known to be connected to receiving waters, then it is a clear fact that small individual systems might have a large effect in aggregate.

b) Does the report include the most relevant peer-revie wed literature on this topic? If not please indicate which references are missing.
As far as I know, yes.

c) Was the reviewed literature cited and summarized cor rectly? If not please indicate where correction or revision is needed.
As far as I know, yes.

Post meeting comments:
The meeting confirmed that the document is well written and makes the case for connection to downstream waters for most wetlands and all streams.
In general, I left this meeting with the idea intact that connection of small streams to rivers is important biologically, chemically and physically. Furthermore, in aggregate, m any small streams act to define the characteristics of the watershed and influences on the str eams and rivers below. This is true for nutrients (adequately supported in document) and organisms (e.g., Fagan 2002).

The section on streams should include ideas from the liter ature on subsidies and feedbacks. For example marine derived nutrients from spawning salmon can influence small streams, but this material also moves down to larger rivers. There is substantial literature on this idea, the report could start with the book on this issue by Polis et al. (2004).
Wetlands are clearly connected to downstream waters. Sever al more references could be put in related to this idea (Devito et al., 1999, Richardson et al., 2004, McCo rmick et al., 2006, Strauss et al., 2009). Biological connections can also move nutrients among isolated water bodies (e.g., Manny et al., 1994, Post et al., 1998).
Some wetlands have very clear and fast connections to downst ream waters, particularly those in more permeable unconsolidated sediments or karst areas (e.g., Malard et al., 1994, White et al., 1995).

Fagan, W.F. (2002) Connectivity, fragmentation, and extinction risk in dendritic metapopulations. Ecology, 83, 3243-3249.Walter K. Dodds, Ph.D.

A-44 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE Devito, K.J., Hill, A.R. & Dillon, P. (1999) Episodic sulpha te export from wetlands in acidified headwater catchments: prediction at the landscape scale. Biogeochemistry, 44, 187-203. Manny, B.A., W. C. Johnson and R. G. Wetzel. (1994) Nutrien t additions by waterfowl to lakes and reservoirs: predicting their effects on productivity and wate r quality. In: Hydrobiologia 279/280:121- 132. (Ed^Eds.
Mccormick, P.V., Shuford, R.B.E. & Chimney, M.J. (2006) Periphyton as a potential phosphorus sink in the Everglades Nutrient Removal Project. Ecological Engineering, 27, 279-289.
Polis, G.A., Power, M.E. & Huxel, G.R. (2004) Food webs at the landscape level, University of Chicago Press. Post, D.M., Taylor, J.P., Kitchell, F.J., Olson, M.H. , Schindler, D.E. & Herwig, B.R. (1998) The role of migratory waterfowl as nutrient vectors in a managed we tland. Conservation Biology, 12, 910-920.
Richardson, W.B., Strauss, E.A., Bartsch, L.A., Monroe , E.M., Cavanaugh, J.C., Vingum, L. & Soballe, D.M. (2004) Denitrification in the Upper Mississippi River: ra tes, controls, and contribution to nitrate flux. Canadian Journal of Fisheries and Aquatic Sciences, 61, 1102-1112.
Strauss, E.A., Richardson, W.B., Cavanaugh, J.C., Barts ch, L.A., Kreiling, R.M. & Standorf, A.J. (2009) Variability and regulation of denitrification in an Upper Mississippi River backwater.
Malard, F., J.-L. Reygrobellet, J. Gibert, R. Chapuis, C. Drogue, T. Winiarsky and Y. Bouvet. (1994) Sensitivity of underground karst ecosystems to human pertur bation - conceptual and methodological framework applied to the experimental site of Terrieu (H erault- France). In: Verh. Internat. Verein. Limnol. 25:1414-1419. (Ed^Eds.)
White, W.B., D. C. Culver, J. S. Herman, T. C. Kane and J. E. Mylroie. (1995) Karst Lands. In: Am. Sci. 83:451-459. (Ed^Eds.)A-45 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE



### James W. La Baugh, Ph.D.

Hydrologist Office of Groundwater U.S. Geological Survey Reston, VA

DEGREES:

Delaware Valley College - 1973 - B.S. Biology; West Virginia University – 1978 - Ph.D. Biology (Limnology)

PROFESSIONAL EXPERIENCE:
Hydrologist, Office of Hydrologic Research, Denver, Colorado, U.S. Geological Survey, July 1978 - March 1995. Hydrologist, Office of Groundwater, U.S. Geological Surv ey, Reston, Virginia, March 1995 to present. Research efforts have been directed at the h ydrological mechanisms controlling chemical fluxes between lakes and wetlands, their watersheds, and the atm osphere, including directly measured contributions by groundwater. This includes investigation of che mical fluxes in saline and non-saline wetlands and lakes in semi-arid environments, and a lake in a humid environment. Research investigations have included work at sites in Colorado, Nebraska, Nort h Dakota, Minnesota, New Hampshire, and Guam. Study of the interaction of lakes and wetlands with groundw ater has included examination of multiple lakes and wetlands within common groundwater flow systems at sit es spanning a climate gradient in midcontinent.

Publications related to the peer review of the EPA draft document have included: examination of various aspects of the water balance of wetlands (Water Resources Bulletin, 22:1-10), variability of wetland characteristics in relation to variable climate (Limnol ogy and Oceanography, 41:864-870), hydrologic functions of prairie wetlands (Great Plains Research, 8: 17-37), and hydrologic considerations in defining isolated wetlands (Wetlands, 23:532-540). Other related publicat ions have pertained to the relation of closed-basin lakes to groundwater (Journal of Hydrology, 86: 279-298; Canadian Journal of Fisheries and Aquatic Sciences, 52:754-767; Water Resources Research, 33: 2799-2812). Materials fluxes in water bodies interacting with streams as well as groundwater have been the subject of other publications (Limnology and Oceanography, 29:322-339; Water Resources Research, 21:1684-1692; chapters in - Mirror Lake: Interactions among Air, Land, and Water, University of California Press, 2009). Finally, some publications pertain to the general topic of the relation of groundwater to surface waters and watersheds (Ground Water, 47:989-1000; Science, 296:1985-1990).James. W. La Baugh, Ph.D.

A-47 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE 

### Peer Review Meeting of EPA’s Draft Report: Connectivity of Streams and Wetlands to Downstream Waters – A Review and Synthesis of the Scientif ic Evidence

Comments submitted by Dr. James W. La Baugh

TECHNICAL CHARGE QUESTIONS: (Note: underlined text in my original responses to the charge questions id entifies critical or essential suggestions)

1. This report concludes that all streams, regardless of f low duration or size, are physically, chemically, and biologically connected to rivers; and these connections, individually or cumulatively, exert a strong influence on the character an d functioning of downstream waters.

a) Are these conclusions supported by the scientific evidence?
The general synthesis of the cited literature provided in the report supports conclusion 1. The document, however, includes some conceptual inconsistencies that would bene fit from resolution and clarification. These items are noted below.

• Page 30, lines 634 to 635 – Figure 3-5 – Because the wetland is at a location where there is a break in slope, the absence of groundwater interaction wit h the wetland is remarkable. The fact there are local, intermediate, and regional flow systems is illustrated by Toth’s work [see figure A4 in Winter et al. (1998) http://pubs.usgs.gov/circ/circ1139/pdf/circ1139.pdf ]. Other figures in Winter et al. (1998) provide cross section diagrams of flow to rivers that includes arrows for local and regional flow, such as for a riverine valley – Figure 22 on page 39.

• If the intent of the use of a figure in this part of the introduction, however, is to indicate flow from groundwater follows shallow, intermediate, and deep flow paths prior to discharge to a river, each representing different amounts of time in transit, a better figure would be something like Figure 3 from Winter et al. (1998). An additional reference for the fact that groundwater r epresenting different flow paths and times in transit discharge to a stream is Modica, E. 1999, Source and age of ground-water seepage to streams. U.S.Geological Survey F act Sheet 063-99, 4 p. http://pubs.usgs.gov/fs/1999/0063/report.pdf

• Page 33, lines 680 to 682 – Are all alluvial aquifers referred to as hyporheic zones? The parenthetical statement equating hyporheic zone with alluvi al aquifer is problematic. To avoid confusing readers, the statement equating hyporheic zone with alluvial aquifers could be deleted.

• Page 38, lines 768 and 769 – The phrase “aquifers contract” is unusual. Does the form ation that is capable of conducting groundwater contract? Perhaps what was meant was that groundwater levels decline.

• Page 42, line 826 – The phrase “This water has can alter the geomorphology...” i s awkward. Revision for clarification would be useful.

• Page 62, line 1195, and page 63, Figure 3-17 – Use of the term ‘impermeable aquifer’ is incorrect.James. W. La Baugh, Ph.D.

A-48 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE An aquifer by definition is “A body of rock that contains suf ficient saturated permeable material to conduct ground water and to yield economically signific ant quantities of water to wells or springs.” Margret Gary, Robert McAfee Jr., and Carol L . Wolf, editors, 1972, ‘Glossary of Geology’, American Geological Institute, Washington, D.C.; o r “An aquifer is a formation, group of formations, or part of a formation that contains suf ficient saturated permeable material to yield significant quantities of water to wells or springs.” S . W. Lohman and others, 1972, Definitions of selected ground-water terms- Revisions and conceptual re finements, U.S. Geological Survey Water-Supply Paper 1988, 21 p.

• Page 62, lines 1194 to 1200 – It would be useful to revise the paragraph to clarify t he key points being made about flow systems while being consistent with co rrect use of technical terms. It is not at all clear why the explanation includes reference to int ermediate or regional flowpaths. Intermediate and regional flow paths occur as a function of groundwater basin depth to width ratio (Toth, J.A., 1963, A theoretical analysis of ground-water flow in small drainage basins. Journal of Geophysical Research, v. 68, p 4795-4811). Also, surface waters with low permeability deposits in area of high topographic relief can receive water fr om beyond the local surface watersheds (Winter et al., 2003, Where does the groundwater in small wa tershed come from? Ground Water, v. 41, p. 989-1000).

• Page 135, line 2731 – Because vagility has the same meaning as capability of movement, is there any reason to use the term? Consider deleting vagility to simplify the text.

b) Does the report include the most relevant peer-revie wed literature on these topics, including evidence of connectivity and isolation? If not please indicate which references a re missing.

• A useful reference regarding the interaction of streams and groundwater is absent from the references – Jones, J.B., and Mulholland, P.J., eds. 2000. S treams and Ground Waters, Academic Press, 425 p.

c) Was the reviewed literature cited and summarized cor rectly? If not please indicate where correction or revision is needed.

• Page 42, line 828; page 175, line 3579; page 307, line 6921 – The name Meybloom in the citation is incorrect. Correct name for this citati on is Meyboom.

• I am not familiar with all of the literature cited in the document regarding the relation of streams to their connection with and influence on downstream rivers, therefore I am not able to judge whether or not all of the cited literature was summarized correctly.

2. This report concludes that open water and wetlands in riparian areas and floodplains of streams and rivers are physically, chemically, and biologically connect ed with the river network, and that their functions exert a strong influence on the char acter and functioning of downstream waters.

a) Are these conclusions supported by the scientific evidence?
The general synthesis of the cited literature provided in the report appears to support conclusion 2. Part of the text pertaining to the relation of open water and ripar ian wetlands to streams and rivers would benefit from clarification, as noted below.James. W. La Baugh, Ph.D.

A-49 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE • Page 2, lines 38 and 39 ; page 10, line 225 – The phrase “...storage of local groundwater sources of baseflow in rivers,” could benefit from clarification. Was the intent of the text that riparian and floodplain wetlands are areas where groundwater flows to the wetlands rather than the adjacent river, thereby intercepting groundwater that otherwise w ould contribute to baseflow?

b) Does the report include the most relevant peer-revie wed literature on these topics, including evidence of connectivity and isolation? If not please indicate which references a re missing.

• No response as this is not a focus of my area of exper tise.

c) Was the reviewed literature cited and summarized cor rectly? If not please indicate where correction or revision is needed.

• I am not familiar with all of the literature cited in the document regarding the relation of open water and wetlands in riparian areas and floodplains of streams and rivers to their connection with and influence on downstream rivers, therefore I am not able to judge whether or not all of the cited literature was summarized correctly.

3. This report concludes that for non-riparian/non-flood plain wetlands that are not connected to the river network through a stream channel (i.e., geographical ly isolated wetlands and wetlands that spill into losing streams), connectivity and isolation vary wit hin a watershed and over time, making it difficult to generalize about their connections to, or isolation from, downstream waters. The literature we reviewed does not provide sufficient infor mation to evaluate the degree of connectivity (absolute or relative) of these non-riparian particular wetlands.

a) Are these conclusions supported by the scientific evidence?
The overall synthesis of the cited literature provided in t he report supports conclusion 3 in general. Parts of the text would benefit from revision for clarification and technical accuracy, as noted below.

• Page 15, lines 336 to 344 – What is the source of the definition of “geographically” isolated? Why is it necessary to distinguish between geographical an d hydrological isolation? The issue of connectivity would seem to be a function of the movement of wa ter (and as noted on page 49, lines 949 -950 – movement of biota) independent of “geography.” The reason for the introduction of the concept of geographic isolation is missing. Also missi ng is a literature citation for the statement that vernal pools and coastal depressional wetl ands are incorrectly referred to as geographically isolated. Why does this distinction matter?

• Page 64, Figure 3-18 – An inconsistency appears to exist between what is shown in part B and the definition of “geographical isolation” on page 15, lines 340 to 342. Why is the nonchannelized swale considered to be upland? By the definition on page 15, the wetland is geographically isolated when completely surrounded by upland. I n order for water to exit the wetland to the swale, would not the swale have to be topogr aphically lower than the wetland proper and be adjacent to it? The point raised here simpl y reinforces the reason for the inclusion of geological isolation in the context of examining connectivity i s unclear.

• Page 218, Table 5-3, second entry – Is soil permeability the major factor controlling whethe r or not a wetland loses water by surface versus groundwater? Wh at about the importance ofJames. W. La Baugh, Ph.D.

A-50 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE topographic setting with respect to the presence of channels o r swales (see Figure 3-18B for example)?

• Page 218, Table 5-3, fourth entry - The connection of a non-riparian wetland to other water bodies through groundwater flow involves a time component. Even i f the groundwater flow system that hydraulically connects a non-riparian wetland wi th an adjacent surface-water body is simply a local flow system, time is a factor related to the influence of the wetland on the adjacent surface-water body. If the flow path is one such that a par ticle of water takes years, decades, or longer to travel down gradient to the surface-water body, that length of time needs to be considered in the determination of how much of an influence the wetland has on the adjacent surface-water body. It might be useful to note that even when the wetlands are connected hydraulically through groundwater time affects the influence of the wetland on adjacent water bodies. The subject of length of time of groundwater flow in relation to wetlands is presented in Winter and LaBaugh(2003) cited in the EPA report.

• Page 241, lines 4981 to 4982 – The use of the term impermeable throughout the document can be confusing. In most cases it seems that the contrast is more likely one of rivers or wetlands in highpermeability terrain in comparison with those in low-perme ability terrain. In the prairie pothole region some water does infiltrate the soil so it would be more precise to indicate the soils and the glacial till comprise low-permeability terrain

.

• Page 250, line 5175 – One factor that can change the chemical characteristi c of prairie pothole wetlands is loss of sediment due to wind erosion during pe riods when wetlands become completely dry. This phenomenon is documented in LaBaugh et al .1996, cited elsewhere in the document. Thus, unaltered wetlands with no surface outlet may also lose nutrients, sediment, and other chemical compounds during such episodes.

• Page 254, lines 5259 to 5265 – One of the key factors affecting connections between pr airie pothole wetlands and streams or river networks is the pres ence of ditches made by human activity. Mention of this is absent from this finding, even though ditching was noted in the supporting text that precedes this section.

• Page 254, lines 5266 to 5269 – Ditching is a key factor enabling sediment, nutrients , and other chemicals that were present in wetlands to move to strea ms or rivers. The presence of a ditch to effect such transport is not conveyed in use of the phrase “Hydrologic sink or source functions of potholes can impact many features...” What exactly is meant by “multiple aspects of flow?” The concern here is that the finding is imprecise relative to w hat has been documented in the literature. In order for water to move across the land surface to a stream or river, either a surface connection needs to be made by a ditch or wetland water levels must rise to spill points in their basins that have a natural topographic path to a stream or river. Only when such hydrologic connections are made will water in the wetlands have the capability of tra nsporting sediment or chemicals to streams.

• Page 256, lines 5311 to 5312 – If the pools lie on impermeable substrates how does water infiltrate to form a shallow flow system? Perhaps the pools lie on low-permeability substrates rather than impermeable substrates. Also, if the substrat e is impermeable, by definition it will not contain a surficial aquifer. A low-permeable substrate c ould contain a shallow groundwater system separated from a deeper regional aquifer by a conf ining bed.James. W. La Baugh, Ph.D.

A-51 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE • Page 270, lines 5617 to 5623 – The content of the paragraph reinforces the need to provi de a better definition of “geographically isolated,” as well as attribution to the source of that definition earlier in the document.

b) Does the report include the most relevant peer-revie wed literature on these topics, including evidence of connectivity and isolation? If not please indicate which references a re missing.

• Arndt and Richardson discuss hydric soil development in prairie pothole wetlands (Arndt, J.L., and Richardson, J.L., 1988, Hydrology, salinity, and hydric soil development in a North Dakota prairie-pothole wetland system. Wetlands, v. 9, p. 93-108) but are not included in the references.

• A useful reference regarding wetland soils and water fl ow in a variety of landscapes is Richardson, J.L., and Vepraskas, M.J., editors, 2001, Wet land soils: genesis, hydrology, landscapes, and classification. Lewis Publishers, Boca R aton, Florida, 417 p.

• Page 283, lines 6053 to 6056 – Entry for the cited literature source is not comple te regarding publication information. The correct, complete entry should be revised as follows –Dickinson, J.E.....2020...Middle San Pedro Watershed, Southeastern Arizona. U .S. Geological Survey Scientific Investigations Report 2010-5126, 36 p. http://pubs.usgs.gov/sir/2010/5126/

• Page 325, lines 7588 to 7593 – Entries for the cited literature source are not comple te regarding the publication information.
The correct entry for the Vining 2002 should be revised as f ollows – Vining, K.C, 2002....Water Years 1981-98. U.S. Geological Survey Water-Resources Investigat ions Report 02-4113, 28 p. http://nd.water.usgs.gov/pubs/wri/wri024113/
The correct entry for Vining 2004 should be revised as follow s Vining, K.C., 2004....North Dakota and Minnesota. U.S. Geological Survey Scientific Investigations Report 2004-5168, 28 p. http://pubs.usgs.gov/sir/2004/5168/

c) Was the reviewed literature cited and summarized cor rectly? If not please indicate where correction or revision is needed.

• Literature pertaining to the overall topic and prairie pothole wetlands was summarized correctly in general. Areas requiring clarification are noted above in 3a

.

• I am not familiar with all of the literature cited in the document regarding the relation of oxbow lakes, Carolina and Delmarva Bays, and vernal pools to th eir connection with and influence on downstream rivers, therefore I am not able to judge whether or not all of the cited literature pertaining to those types of wetlands was summarized cor rectly.James. W. La Baugh, Ph.D.

A-52 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE 4. This report concludes that while the influence of a particular stream or wetland on downstream waters might be small, the aggregate contribution by an entire class of streams or wetlands (e.g., all ephemeral streams in the river network, or a cluster of small wetlands) might be substantial.

a) Is this conclusion supported by the scientific evi dence?

• In the section 6 of the document containing the set of conclus ions (pages 266 to 271), the conclusion noted as 4 above was not presented. Nor was a four th conclusion presented in Executive Summary at the beginning of the report. The absence of a fourth conclusion in the report, accompanied by supporting statements of key findings to support that conclusion, make answering this question and the following questions problem atic.

b) Does the report include the most relevant peer-revie wed literature on this topic? If not please indicate which references are missing.

• Insufficient information was provided to enable an answer to the question.

c) Was the reviewed literature cited and summarized cor rectly? If not please indicate where correction or revision is needed.

• Insufficient information was provided to enable an answer to the question.

Post meeting comments

In Reference to Charge Question Number 3, I offer the fol lowing text as one possible solution to the dilemma posed by use of the term non-riparian and channel or igin wetlands.
EPA connectivity panel - wetland classification note and sugges tion
One document that discusses various aspects of wetlands in relation to hydrological characteristics is
Winter, T.C., and Woo, M-K. 1990. Hydrology of lakes and we tlands, p. 159-187, in Wolman, M.G., and Riggs, H.C., (eds.) Surface Water Hydrology. The Geology of North America, volume O-1. Geological Society of America, Boulder, Colorado.
In this document the authors note that existing classifica tions are not easily unified. In Winter and Woo (1990), a variety of lakes and wetlands were examined in the c ontext of geologic settings, hydrologic processes controlling water balances, and physiographic sett ings.
In the EPA connectivity draft, the need to define channel or igin wetlands is not compelling. If channel origin wetlands were simply thought of in terms of being the headwate rs of a river, the need to include them as a separate category is eliminated. They would fall into the category of being associated with a river. The resul t would be two classes of wetlands, those associated dire ctly with rivers, riverine wetlands (borrowing from Winter and Woo) - river headwater, riparian, and floodplain wetlands? and those not directly associated with rivers, non-riverine wetlands. Use of these two simple te rms, riverine and non-riverine wetlands, also makes a distinction among wetlands: the first, those wetlands mor e likely to be directly connected by a surface waterJames. W. La Baugh, Ph.D.

A-53 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE connection with a river, and second, those wetlands less li kely or unlikely to be directly connected by a surface water connection with a river. I suggest you substitute river headwater wetlands for channel origin wetlands in the text and include them in text pertaining to riparian and floodplain wetlands. Then substitute non-riverine wetlands for non-riparian wetlands throughout the doc ument. Such revision might solve the wetlands classification dilemma discussed on January 30, 2012 d uring the panel meeting.
As an aside, Plate 2 from Winter and Woo (1990) is a nice p ortrayal of the fact that about half of North America is not humid. A figure for the lower 48 states de rived from that plate is Figure 14, page 21 in
Reilly, T.E., Dennehy, K.F., Alley, W.M., and Cunningham, W .L., 2008. Ground-Water Availability in the United States. U.S. Geological Survey Circular 1323, 70 p. http://pubs.usgs.gov/circ/1323/
although the figure in Reilly et al. (2008) does not feature the gradients within the semi-arid to arid region shown in the plate of Winter and Woo (1990).

Comment on organization of the document: It would be useful to consider reorganization of the docum ent. Conceptual framework material regarding connectivity and influence appearing in both the stream (sec tion 4) and wetlands (section 5) sections could be moved to section 3 (A conceptual framework) for consistency and clarity of presentation. Readers could then be referred to aspects of this common framework as needed in subsequent discussion of the relation of streams and wetlands to rivers.
One way of organizing a synthesis document is to present the conceptual framework as the main body of the text, with examples from different settings shown as ‘boxe s’ or ‘sidebars’ – see Winter et al. (1998) as an example - http://pubs.usgs.gov/circ/circ1139/ [this reference is cited in the current version of the document]. Another way of organizing a synthesis document is to presen t the conceptual framework as the main text, using ‘boxes’ interspersed to highlight particular technical nuances, with case studies as part of the text appearing after presentation of the conceptual framework – see Healy et al. (2007) as an example - http://pubs.usgs.gov/circ/2007/1308/

Comment regarding the definition of groundwater in the glossar y: The definition is correct. One of the other reviewers suggest ed labeling all subsurface as groundwater. Water in the unsaturated zone is not groundwater. See also page 4 of Heath, R.C., 1983, Basic ground-water hydrology. U.S. Geological Survey Water Supply Paper 2220, 84 p. http://pubs.usgs.gov/wsp/wsp2220/

Comment regarding use of the term watershed: The document never clearly states that the term watershe d as used in the report refers to surface water watersheds. It would be useful to note this convention when the word is first used. I may have missed something, but did not find groundwater watersheds mentioned in the text. Somewhere in the introduction, readers would benefit from a brief statement that groundwa ter watersheds also exist but might not coincide with surface water watersheds. Furthermore the boundaries of those watersheds can change over time in response to changing hydrologic conditions. This subject may fit in when the concept of groundwater flowJames. W. La Baugh, Ph.D.

A-54 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE systems is introduced. As noted in my first comment rega rding question 1. Figure 3-5 is inaccurate in its portrayal of local, intermediate, and regional flow syst ems. It would be better to use Toth’s figure to do that . A local flow system is one in which groundwater flows from a water table high to an adjacent lowland. An intermediate flow system is one in which groundwater flows from a water table high to a lowland that is not immediately adjacent to the water table high. If the depth to width ratio of the aquifer is large enough, a regional flow system may also be present. Topographic divi des do not always coincide with water table highs. Variability in the presence or absence of coincidence of surface water and groundwater watersheds is documented in Winter, T.C., Rosenberry, D.O., and LaB augh, J.W., 2003, Where does the ground water in small watersheds come from? Ground Water, volume 47, number 7, pages 989-1000.

Comment about illustration of hydrologic landscapes of the conti nental United States and Alaska and Hawaii: Mention was made during the discussion that it might be use ful to provide readers with the spatial context of ecoregions and hydrologic landscapes. Figure 8 on page S79 of Woll ock et al., 2004 cited in the EPA document is the one that was suggested. It is also possible that inclusion of this figure, as well as the text needed to explain the content of the figure, might distract fr om the main focus of the conceptual framework because of the detail involved.

Comment about illustrating effects of pumping on groundwater f low paths interacting with a stream: Figure C-1 on page 15 of Winter et al. (1998) shows effect of a pumping well on changes in groundwater flow paths.

Note about example illustrations: Sources of hydrologic processes or connections (flow path) ill ustrations are provided herein. These are provided simply as examples of ways flow processes or connec tions have been illustrated in a variety of settings apart from the more general diagrams used from the W inter et al. (1998) reference in the EPA connectivity document.
[Note: the following two references are key citations for Florida wetlands that were not included in the EPA document, but should be. Essential references ]

[Essential reference ] Haag, K.H., and Lee, T.M., 2010, Hydrology and ecology of fr eshwater wetlands in central Florida – A primer. U.S. Geological Survey Circula r 1342, 138 p. http://pubs.usgs.gov/circ/1342 [Figure B-1, page 17 – flow in relation to seepage wetlands; F igure 5, page 21 – flow in Florida karst terrane]

[Essential reference ] Lee, T.M., Haag, K.H., Metz, P.A., and Sacks, L. A., 2009, Comparative Hydrology, Water Quality, and Ecology of Selected Natural and Augme nted Freshwater Wetlands in West-Central Florida. U.S. Geological Survey Professional Paper 1758, 152 p

. http://pubs.usgs.gov/pp/1758/ [Figure 1, page 4 – water budget of isolated wetland with fluc tuating water level; Figure 11, page 24 – example of flow system in relation to wetland]James. W. La Baugh, Ph.D.

A-55 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE Buszka,P.M., Cohen, D.A., Lampe,D.C., and Pavlovic, N.B ., 2011, Relation of Hydrologic Processes to Groundwater and Surface-Water Levels and Flow Directions in a Dune-Beach Complex at Indiana Dunes National Lakeshore and Beverly Shores, Indiana. U.S. Geologi cal Survey Scientific Investigations Report 2011-5073, 75 p. http://pubs.usgs.gov/sir/2011/5073/ [Figure 3, page 5 – Effect of tile drain on flow]

[Essential reference ] Tribble, Gordon, 2008, Ground Water on Tropical Pacific Isla nds—Understanding a Vital Resource. U.S. Geological Survey Circular 1312, 35 p. http://pubs.usgs.gov/circ/1312 [Page 4 – Figure showing surface and groundwater flow paths; P ages 10 and 11 - various groundwater flow settings ]
Faunt, C. C., editor, 2009, Groundwater availability of the C entral Valley Aquifer, California. U.S. Geological Survey Professional Paper 1766, 225 p. http://pubs.usgs.gov/pp/1766 [Figure A9, upper part, page 21 – surface and groundwater flow paths in the Sacramento Valley]

Barlow, P.M., 2003, Ground Water in Freshwater-Saltwater Environments of the Atlantic coast. U.S. Geological Survey Circular 1262, 113 p. http://pubs.usgs.gov/circ/2003/circ1262/ [Figure 3, page 4 – Surface water and groundwater flow paths in the Atlantic coastal plain]
Izbicki, J.A., Johnson,R.U., Kulongoski, J., and Predmore, S., 2007, Ground-Water Recharge from Small Intermittent Streams i n the Western Mojave Desert, California. Chapter G in Stonestrom, D.A., Constantz, J., Ferré,T.P.A. an d Leake, S.A., editors, 2007, Ground-Water Recharge in the Arid and Semiarid Southwestern United States. U.S. G eological Survey Professional Paper 1703 http://pubs.usgs.gov/pp/pp1703/ The entire report is a large document so chapter link i s provided below. http://pubs.usgs.gov/pp/pp1703/g/pp1703g.pdf [Figure 4, page 163 – hydrologic features of intermittent stre ams in the Mojave Desert]

Planert, M., and Williams, J.S., 1995, Ground Water Atla s of the United States - California, Nevada. U.S.Geological Survey Hydrological Atlas 730-B, http://pubs.usgs.gov/ha/ha730/ch_b/gif/b025.gif (Also available as an Adobe Illustrator eps file) [Figure 25 – block diagram of basin types showing groundwater flow relations to types of playas]James. W. La Baugh, Ph.D.

A-56 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE * Documents referred to in general discussion, but not cri tical for the EPA document, except where noted :

Document related to the fact the concept of average conditions is outdated
Milly, P C. , J Betancourt, M Falkenmark, R M Hirsch, Z W Kundzewic z, D Lettenmaier, and Ronald J Stouffer , 2008: Stationarity is dead: Whither water management? Science
, 319(5863) , 573-574.

Document related to conceptual framework of geomorphology in relation to milldams

Merritts, Dorothy, Rahnis, Michael, Walter, Robert, H artranft, Jeff, Cox, Scott, Scheid, Chris*, Potter, N oel*, Jenschke, Matthew*, Reed, Austin*, Matuszewski, Derek*, K ratz, Laura*, Manion, Lauren*, Shilling, Andrea*, Datin, Katherine*, 2011 (in press), The rise and fall of Mid-Atlantic streams: Millpond sedimentation, milldam breaching, channel incision, and stre am bank erosion: Reviews in Engineering Geology, special issue on “The Challenges of Dam Removal an d River Restorations”, editors Jerome V. DeGraff and James E. Evans.

Document related to hydrological and biological interrelations pertaining to removal of invasive species from riparian zones

Shafroth, P.B., Brown, C. A., and Merritt, D.M., edi tors, 2009, Saltcedar and Russian Olive Control Demonstration Act Science Assessment. U.S. Geological Su rvey Scientific Investigations Report, 2009-5247, 143 p. http://pubs.usgs.gov/sir/2009/5247/

Document pertaining to analysis of changing hydrologic condition s in relation to potential for Devils Lake to spill to a river

Vecchia, A.V., 2008, Climate simulation and flood risk analys is for 2008-40 for Devils Lake, North Dakota: U.S. Geological Survey Scientific Investigations Report 2008- 5011, 28 p. http://pubs.er.usgs.gov/usgspubs/sir/sir20085011

.
Document that discusses the relation of hydraulic conductivity to presence/absence of groundwater watershed divides

Winter and LaBaugh (2003) cited in the EPA document. The so urce of the information regarding the importance of moderate to highly permeable versus poorly per meable geologic substrates is Haitjema, H.M., 1995. Analytic element modeling of groundwater flow. Academic P ress, San Diego, California.

Documents pertaining to overviews of wetlands in the Nebraska Sandhills

[Essential reference] Novacek, J.M., 1989, The water and wetland resources of the Nebraska Sandhills, in van der Valk, A., ed. Northern Prairie Wetlands, Iowa S tate University Press, Ames, Iowa, p. 340-384.James. W. La Baugh, Ph.D.

A-57 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE Gosselin, D.C., 1997, Major-ion chemistry of compositional ly diverse lakes, Western Nebraska. U.S.A.: implications for paleoclimatic interpretations, Journal of Paleolimnology, 17:33-49.

Document related to presence and characterization of pl ayas:
[Essential reference] Wood, W.W., 2002, Role of ground wat er in geomorphology, geology, and paleoclimate of the southern High Plains, USA: Ground Water, v. 40, p. 438 -447.

Document providing details about the dynamic nature of hydrologica l and biological interactions of prairie wetlands

Winter, T.C., ed., 2003, Hydrological, chemical, and biologi cal characteristics of a prairie pothole wetland complex under highly variable climate conditions - The Cottonwood Lake area, east-central North Dakota: U.S. Geological Survey Professional Paper 1675, 109 p. http://pubs.usgs.gov/pp/1675/report.pdf

Document related to movement of nutrient plume from infiltr ation ponds to nearby lake

McCobb et al., 2003, Phosphorus in a Ground-Water Contaminant Plume Dischargi ng to Ashumet Pond, Cape Cod, Massachusetts, 1999. U.S. Geological Survey Water- Resources Investigations Report 02-4306, 69
p. http://pubs.usgs.gov/wri/wri024306/

Document related to irrigation canal recharge of groundw ater as source of baseflow in rivers inhabited by endangered fish species

Ely, D.M., 2003, Precipitation-Runoff Simulations of Curre nt and Natural Streamflow Conditions in the Methow River Basin, Washington. U.S. Geological Survey Water -Resources Investigations Report 03-4246, 43 p. http://pubs.usgs.gov/wri/wri034246/A-59 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE



### Mark C. Rains, Ph.D. Associate Professor University of South Florida. Tampa, FL

Mark Rains is an ecohydrologist with a B.A. in Ecology, Beha vior, and Evolution (UC San Diego 1990), an M.S. in Forestry (University of Washington 1994), and a Ph.D . in Hydrologic Sciences (UC Davis 2002). He has nearly 20 years experience in the public and private se ctors in the science, policy, and management of wetlands and rivers, including extensive experience in the functional assessment, restoration, and management of degraded wetlands and rivers. He currently is an Associate Professor of Ecohydrology in the Department of Geology at the University of South Florida, Tampa, Florida. He is also the President of Coshow Environmental, Inc. in Temple Terrace, Florida, and the Associate Editor for Aquatic Ecology for the Journal of the American Water Resources Association.

Dr. Rains’ research is focused on (a) local- and landsc ape-scale hydrological connectivity, (b) the roles that hydrological processes play in governing ecosystem structure an d function, and (c) the roles that science plays in informing law and policy. He pursues these efforts in a variety of surface-water and shallowgroundwater environments, including depressional wetlands, headwa ter streams and mainstem rivers, and mangroves and lagoons. Dr. Rains has additional service-rel ated interests in sustainable water-resources development in poor, rural communities in Latin America and the Caribbean Basin, and extensive experience in consensus building at the intersection of scie nce and policy in wetland regulatory programs, including past and ongoing work related to providing the scien tific justification underlying the federal definition of “waters of the US” subject to regulation under the Clean Water Act. For the latter, he was awarded U.S. Environmental Protection Agency Scientific a nd Technological Achievement Awards in both 2007 and 2009.

Dr. Rains is the author or co-author of more than 25 peer- reviewed papers, more than 30 technical reports, and five peer-reviewed teaching tools. He also is the author or co-author of more than 50 posters/ presentations delivered at a variety of regional, nationa l, and international meetings and university colloquia.Mark C. Rains, Ph.D.

A-61 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE 

### Peer Review Meeting of EPA’s Draft Report: Connectivity of Streams and Wetlands to Downstream Waters – A Review and Synthesis of the Scientif ic Evidence

Comments submitted by Dr. Mark C. Rains

REVIEWER COMMENTS ON CONCEPTUAL FRAMEWORK:

SUMMARY The key flaw in the document is that you arbitrarily brea k the landscape into three components, make the focus of the document on the individual discussions of those thre e components, and therefore make it difficult for you to show the inherent connectivity across these component s. To counter this, I think that you should make the conceptual framework the highest order of organization in this document. The conceptual framework should be the central point of the document—the re st of the document should be to support and better explain this conceptual framework. Then conceptual f ramework should start with the premise that all components of the landscape are connected, and that what di ffers is the degree to which they are connected and the importance of those connections to downstream syste ms. You should clearly explain hydrological, chemical, and biological connectivity—but especially hydrological connectivity—in the context of the relevant literature (e.g., Pringle 2001, Pringle 2003a, Pringle 2003b, Freeman et al., 2007), using clear diagrams to illustrate that connectivity extends from ridges to reefs and connects all of the individual elements discussed in the document. You also should clearly explain the broader conceptual framework that you build relating to the five functions or roles that wetlands and streams play (e.g., source, sink, etc.). Last, you shoul d explain how this landscape-scale connectivity means that the cumulative effects of many wetlands and streams can be large, even if the individual effect of one w etland or stream may be small. This, then, should the foundation to which you return throughout the document, alwa ys reminding the reader about how the supporting information in each of the three individual componen ts relates to this conceptual model, and showing specifically how connections and their downstream effec ts are clear in some cases and not so much in others.

DETAILED COMMENTS General Comment: Throughout the document, there were terminol ogy problems that make the basic conceptual framework and the scientific evidence difficult to follow. The first problem relates to the various uses of the terms headwaters, headwater streams, and stre ams. These are often used interchangeably, even though they are not commonly used interchangeably, and are not def ined as such in the Glossary. To improve clarity, the standard definitions in the Glossary should be used throughout the text. The second problem relates to the use of connectivity. At times, it is used i ndependently; at other times, it used following a specific modifier (e.g., biological connectivity). This would not be a problem if independent usage implied any or all kinds of connectivity. However, that doesn’t seem to be t he case; rather, independent usage often seems to imply hydrological connectivity, and perhaps even surface-wate r connectivity (e.g., l. 594-597). To improve clarity, independent usage should refer to the existence of any kind of connectivity, while modified usage should refer to the existence of a specific kind of connectiv ity.Mark C. Rains, Ph.D.

A-62 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE General Comment: There are significant problems with some o f the technical aspects of the conceptual framework, particularly in relation to how water gets from uplands to wetlands or streams or between wetlands and streams. This is a critical part of the conc eptual model, because it underlies the complex pathways and controls on hydrological connectivity. Lacking a prope r conceptual framework in this regard, the document will fail to make a strong case not only for h ydrological connectivity but also for all types of connectivity at spatial and temporal scales that matter in a regulatory environment. I make numerous specific comments in relation to this below.
l. 522-523: Rains et al. (2006, 2008) would be good references for this condition.

l. 534-536: This sentence concludes that water flows “downhill”. This isn’t actually true. Water flows downgradient, where gradient is primarily due to differe nces in elevation (i.e., the downhill part of downgradient) and pressure. Pressure plays important roles i n surface-water flows, but plays even more important roles in groundwater flows, including groundwa ter flows as they relate to the conceptual framework and the scientific evidence presented throughout each of the subsequent chapters.

l. 575-577: This is not the correct federal definition of a we tland. The federal definition of a wetland is a regulation—which carries the full force of law—that can be found at 33 CFR 328.3(b): “The term ‘wetlands’ means those areas that are inundated or saturated by surf ace or ground water at a frequency and duration sufficient to support, and that under normal circumstances do support, a prevalence of vegetation typically adapted for life in saturated soil conditions. Wetlands gener ally include swamps, marshes, bogs, and similar areas.” This is very similar to a definition used late r in the document (l. 3455-3456). What the authors refer to here is the Corps of Engineers Wetlands Delineation Manual (U SACE 1987), which is guidance—which does not carry the full force of the law—on how to delineate a we tland and not a regulation—which does carry the full force of the law—on how a wetland is defined. One benefi t of using the correct federal definition of a wetland found at 33 CFR 328.3(b)—which is more generic and incl usive, with rather vague boundaries—is that you won’t struggle so much in trying to explain what yo u are considering a wetland in the riparian and floodplain wetland discussion (l. 3531-3540).
l. 613-614: There are two primary types of aquifers: unconfined and confined. In unconfined aquifers, the upper surface of the saturated zone is defined by the water table ; in confined aquifers, the upper surface of the saturated zone is defined by the confining layer, and the w ater in the saturated zone is under pressure and will rise up to the potentiometric surface if the confining layer i s perforated (e.g., by a piezometer or even by a natural fracture, as occurs at many springs). See my comm ent titled “Figure 3-4”, below.
l. 614-615: This is an inadequate definition of groundwater, bec ause it leaves the issue of water in the unsaturated zone undefined. I suggest that you define groundwater as all water underground, be it in the unsaturated or saturated zones, then distinguish between the two when necessary by referring to them specifically as unsaturated-zone (or vadose-zone) groundwate r and saturated-zone groundwater, respectively.
l. 615-616: There are many saturated deposits that we do not c ommonly call aquifers. Clays, for example, are commonly saturated but are not commonly called aquifers, and are instead commonly called aquitards, perching layers, or confining layers, depending upon the role they are playing. Perhaps you mean highly permeable instead of just permeable, but if so then you chose poor examples as soil could be anything,Mark C. Rains, Ph.D.

A-63 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE including low-permeability clay-rich soils, and rock h as extremely low primary permeability, though it can have relatively high secondary permeability if there are abund ant and well-connected fractures. You might instead say: “Relatively highly permeable materials (e. g., sand and gravel) that are saturated and in which groundwater is stored and transmitted are referred to as aquifers.”
Figure 3-4: This is an oversimplification that affects your conceptual framework. I suggest that you show both unconfined and confined aquifers here. I know that this is a bit confusing, but is critically important in understanding connectivity. Many waters are hydrologically connecte d by unconfined aquifers, but many others are hydrologically connected by confined aquifers, esp ecially where confined aquifers are perforated and regional groundwater discharges to streams and rivers (e.g., Kish et al., 2010) or surface water recharges regional groundwater (e.g., Sinclair 1977).
l. 628-630: Kish et al. (2010) would a good reference at the end of the last clause as they showed that the vast majority of flow in the Hillsborough River, west-central Florida, was groundwater discharged from the Floridan aquifer, primarily at a single spring.
l. 631-648, Figure 3-5: I’ve lumped the text and figure here, becaus e they are so closely related.
There are quite a few things wrong here, which stem from a n oversimplification on the part of Winter et al. (1998), which is the referenced paper but not the original work, and a misinterpretation on the part of these authors. The original work, cited in Winter et al. ( 1998), was by Toth (1963). Haitjema and Mitchell-Bruker (2005)—who, incidentally, were students of Toth’s—showed that Tot h (1963) was correct, but only for certain cases such as the special case in which he was working. The truth is somewhat more complicated, and relates to important controls by climate and geology, especially geol ogic heterogeneity. Still, you might decide to keep this, subject to some comments below, because there’s no thing really wrong with using terms like local and regional groundwater flows. (Although I must admit that I ’ve never understood the distinction between intermediate and regional groundwater flows.) If you do, howeve r, you need to revise Figure 3-5, which is incorrect. Local groundwater flows are from a local high to a local low. This is the case in Figure 3-5. However, intermediate and regional groundwater flows are la rger in spatial scale and cross one or more groundwater divides (i.e., they cross under one or more poten tial local groundwater flows). This is not the case in Figure 3-5; the intermediate groundwater flow is fr om a local high to a local low (i.e., it’s another local groundwater flow) while the origin of the regional groundw ater flow is a bit unclear.
Regardless, I think that this is an incomplete conceptua l model of flow from uplands to rivers and wetlands. There actually are four pathways that water can take f rom an upland to a river or wetland (Figure 1; Knighton 1998).

• Saturated Groundwater Flow (Pathway 1 in Figure 1): This i s common flow of groundwater through the saturated zone. In this case, this would be an example of a local groundwater flow, though in other cases these might be intermediate or regional groundwater flows.

• Throughflow (Pathway 2 in Figure 1): This is quick flow thr ough the unsaturated zone. This is commonly rapid flow through preferential flow paths, which can be so il cracks, animal burrows, or naturally formed soil pipes.Mark C. Rains, Ph.D.

A-64 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE • Infiltration-Excess Overland Flow, or Hortonian Overland Fl ow (Pathway 3 in Figure 1): This is overland flow where there is an unsaturated zone between the overland flow and the water table. This occurs when the rainfall rate exceeds the infiltration rate, a thi n layer of saturation blankets the surface, and excess rainfall runs off.

• Saturated Overland Flow, or Dunne’s Mechanism of Overland F low (Pathway 4 in Figure 1): This is overland flow where the water table has risen to the surface and subsurface storage is full. This area varies through the course of the year and a given storm, giving rise to the term variable source area.
This is a more complete and technically correct conceptua l model on which to base your reasoning. This is particularly true, because this emphasizes an important poi nt, which I don’t think comes through in the document, which is that headwaters continue from the headwat er stream up to the summit of the adjacent hillslope. Headwater streams and adjacent hillslopes a re, in fact, integrally connected, to the extent that headwater streams cannot exist absent the adjacent hillslop es. This point is central to the argument made by Nadeau and Rains (2007), and can be seen (explicitly, in som e cases) in the way that they discuss the references therein. (See, specifically, the way they dis cuss Triska et al., [2007] and Meyer et al., [2007], though both are referred to not as “2007” but, rather, as “ this issue”.)
l. 676-679: Your definition of alluvium is somewhat confusing, in t hat there is a separate item in the list that comprises “at the base of a mountain”, which could be eit her an alluvial fan (i.e., a fan of deposits deposited by water flowing off of a hillslope and into a valley) or a colluvial fan (i.e., a fan of deposits deposited by gravity pulling dry materials down a steep hillslope).

Figure 1. This is copied from Knighton (1998). The text a bove refers to this figure.Mark C. Rains, Ph.D.

A-65 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE l. 720-722: You might follow this with a specific example. For exa mple, wetlands can be seasonally isolated, connected by groundwater flows, and connected by surface-water a nd groundwater flows (Rains et al., 2006, 2008).
l. 794-796: A good reference for the first three items in thi s list would be Hammersmark et al. (2008); a good reference for the fourth and last item on this list would be Wolman and Miller (1960).
l. 896-899: A stream or wetland also can provide different fu nctions at the same time, depending upon perspective. Rains et al. (2006) showed evidence that vernal pools simultaneously serve as a sink for nitrogen and a source for organic carbon, because nitrogen-rich/orga nic carbon-poor groundwater flows into vernal pools, the nitrogen is uptaken and converted to organic carbon, and nitrogen-poor and organic carbon-rich surface water and groundwater flow out of the vernal pools.
l. 990-993: The parenthetical list of “internal components” inc ludes “alluvium” and “geologic materials”, but alluvium is a geologic material. I suggest omitting “geologi c materials”.
l. 1016-1018: Water-borne contaminants can still be transported from a closed-basin depression to a river through groundwater flow.
l. 1053-1055: Rains et al. (2006, 2008) would be good references for t his condition.
l. 1056-1059: You might also mention that downstream transport of seeds and/or propagules and seasonal flooding of riparian/floodplain wetlands is essential fo r the recruitment of vegetation, especially willows and cottonwoods (McBride and Strahan 1984, Scott et al., 1996, Ma honey and Rood 1998).
l. 1079-1222: I think that this entire discussion could be improved if it were integrated to include both climate and watershed characteristics at the same time, using Winter (2001) and Wolock et al. (2004) as the basis for the discussion. This is especially apparent when you compare t he different the different hydrographs, which you try to do only in the context of climate, but are, in fa ct, the result of climate operating on watershed characteristics, an inconvenient fact that you end up having to mention briefly in l. 1134-1135.
l. 1080-1081: I don’t think that this statement is technically t rue, given the importance of geology, topography, and land cover. It’s probably better to say that “Climate determines the amount, timing, and duration of water available to the watershed.”
l. 1092-1093: How are you defining water surplus? Is it precipitat ion minus evapotranspiration? If so, then this sentence isn’t always true because the highest water surplus in snowy catchments is in mid-winter, when snowfall is greatest and evapotranspiration is negligible, bu t flow is low because most of the water is locked up in the snowpack storage.
l. 1098-1104: The first clause in the first sentence is only half true. See the descriptions of the two types of overland flow in my comment titled “l. 631-648, Figure 3-5” above. B ecause you start with only a half true premise, your subsequent examples are not altogether true. For example, overland flows can occur simply where water tables are shallow, regardless of rainfall intensities.Mark C. Rains, Ph.D.

A-66 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE l. 1194-1200, Figure 3-17: I’ve lumped the text and figure here, becaus e they are so closely related. The paragraph uses incorrect terminology. See my comment titled “l. 615-616” above. There isn’t such a thing as an “impermeable aquifer”, because an aquifer must be able to store and transmit water, by definition, and a deposit that is impermeable cannot do either, also by defi nition. Similarly, all aquifers are permeable, so the term “permeable aquifer” is redundant. Also, permeabilit y is just one part of what controls the direction and rate of groundwater flow. Hydraulic head is the other part. Therefore, the entire discussion here about how permeability controls the direction of groundwater flow is no t entirely correct. However, the general themes in the paragraph and in the figure are not entirely inco rrect, except for the incorrect terminology in both the paragraph and the figure legend and explanation. Therefore, I think this can all be rescued, if the terminology is corrected and the controls on the direction and rate of groundwater flow are better explained. This can all be done better if you adopt the more complete and technically c orrect conceptual model I suggest in my comment titled “l. 631-648, Figure 3-5”.

l. 1223-1318: This is a bit of awkward section because distribution is equally controlled by climate and geology, so this isn’t really a standalone factor equal in importance to climate and watershed characteristics. You should probably state as much at the start, and could readily reference Tihansky (1999) as an example, as she shows that climate and geology control the distribution of s inkhole depressions in Florida, most of which are wetlands or lakes, particularly concentrating them in west-central Florida.
l. 1274-1278: This is not exactly true. Floodplains typically don’t flood uniformly laterally away from the channel; rather, floodplains typically flood by engaging sec ondary and other paleochannels, sometimes by groundwater upwelling, other times by overbank flow (Tockner et al., 2000). These secondary and other paleochannels are all over the floodplain, and can be at the e xtreme edge of the floodplain complex, and the effect is that riparian/floodplain wetlands do not connect s trictly as a function of distance from the main channel.
l. 1408-1413: Another excellent example is Hammersmark et al. (2008) , who showed that the restoration of rivers, where incised channels are backfilled and the histo ric channels are reoccupied on the historic floodplains, can decrease the duration of dry season basefl ow by (a) raising the alluvial water table and therefore increasing losses to evapotranspiration and (b) decreasing the hydraulic gradient and therefore the flux of water from the alluvial aquifer to the channel.Mark C. Rains, Ph.D.

A-67 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE TECHNICAL CHARGE QUESTIONS:

1. This report concludes that all streams, regardless of f low duration or size, are physically, chemically, and biologically connected to rivers; and these connections, individually or cumulatively, exert a strong influence on the character an d functioning of downstream waters.
a) Are these conclusions supported by the scientific evidence?
b) Does the report include the most relevant peer-revie wed literature on these topics, including evidence of connectivity and isolation? If not please indicate which references a re missing.
c) Was the reviewed literature cited and summarized cor rectly? If not please indicate where correction or revision is needed.

SUMMARY The conclusions are supported by the scientific evidence provided . This is the easiest task for the authors, because hydrological and ecological connectivity are fundamental te nets for these systems. However, I do have comments regarding some flaws and/or inadequacies in t he scientific evidence provided as justification. (See, also, the detailed comments related to the conceptual framework in the section titled “Additional Reviewer Comments” below.)

DETAILED COMMENTS
General Comment: There is incomplete discussion of perennial tributaries that are disconnected from perennial mainstems by seasonal or ephemeral reaches. Thi s commonly occurs in the West, where tributaries are often perennial in the mountains but lose rapidly and are intermittent or ephemeral on the alluvial fans (Izbicki 2007). Furthermore, there is no discussion at all o f closed basins that lack any kind of navigable water at all. I don’t know about now, but I do know that a few ye ars ago, the U.S. Army Corps of Engineers (Corps) Albuquerque District was calling these isolated basins not subject to federal jurisdiction under the Clean Water Act (Parenteau 2004-2005). This document should provi de clearly articulated evidence, one way or another, toward connectivity in these contexts to better e nable decision-makers to resolve this policy conflict. Nadeau and Rains (2007) foresaw this, and separat ed this case out for special attention. Something like that might be called for here, too.
l. 1492-1537: This entire section would be greatly strengthened if you would include a review of some of the papers that show that hydrological and ecological connectivity a re central tenets of stream hydrology and ecology. Some examples might include the Four-Dimensional Nat ure of Lotic Ecosystems (Ward 1989), the River Continuum Concept (Vannote et al., 1980), the Serial Dis continuity Concept (Stanford et al., 1988, Ward and Stanford 1995, Stanford and Ward 2001), and the Fea tured Collection of JAWRA devoted to this very topic (Nadeau and Rains 2007 and references therein; No te: The Nadeau and Rains 2007 referenced in this specific instance is different than the Nadeau and Rains 2007 referenced throughout the document and elsewhere in this review. See Additional Literature Cited below.). Doing so will accomplish two objectives: (1) make it clear from the outset that we’ve long since acc epted hydrological and ecological connectivity asMark C. Rains, Ph.D.

A-68 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE fundamental tenets and (2) provide critical context for much of the remaining discussion of the specific examples (e.g., l. 2174-2175).
l. 1517-518: This sentence is redundant with the following parag raph. I suggest omitted this sentence here altogether, and relying entirely upon the following paragraph to make the point.

l. 1697-1698: Water scours channels, not sediments.
l. 1698-1701: Add “reducing channel capacity” to the list.
l. 1710-1716: Lane (1955) is an excellent way to understand and expl ain reach-scale flow-sediment dynamics. Because Lane (1955) is often difficult to track down, you migh t also cite Bull (1991), who republished the findings of Lane (1955).
l. 1977-1978: The following two comments relate to nutrient subsi dies, which you mention, though not specifically by name, elsewhere in the document (e.g., l. 2174-2175). Drs. Dodds and Wipfli may also mention nutrient subsidies. Therefore, you may choose to consi der the following two comments here or elsewhere in a separate paragraph dealing specifically wit h nutrient subsidies.
l. 1977-1978: You might consider adding a paragraph here on seasonal nitrate fluxes in Mediterranean and other similar seasonally arid environments. Such seasonal f luxes have been repeatedly observed and explained as an asynchrony between hydrological and biological processes in annual grasslands in Mediterranean and other similar seasonally arid environments (Tate et al., 1999, Holloway and Dahlgren 2001, Rains et al., 2006). Quoting from the latter: “Upland annual grasses senesce in the dry season. However, microbial activity continues, nitrogen is mineral ized, and nitrate accumulates in the upland soils. Annual grasses germinate early in the wet season, but do no t develop substantial biomass until the middle- to late-growing season (i.e., March–April). Thus, during the e arly-season storm events, there is little biological demand for nitrate and it is readily leached from the uplan d soils into the perched groundwater that ultimately discharges to the vernal pools. Later in the wet season, much of the nitrate in the upland soils has been flushed and the upland annual grasses are flourishing, which produces a large biological demand for the remaining nitrate. Therefore, the amount of nitrate leaching into the perched groundwater and subsequently discharging to the vernal pools decreases.”
l. 1977-1978: You might consider adding a paragraph here on alder-fi xed nitrogen subsidies in wetlands and streams. For example, Shaftel et al. (2010) showed that ni trogen concentrations are correlated with alder cover in salmon-bearing headwater streams on the lower Kenai Peninsula, Alaska. We are now conducting follow up work to determine if all alder patches are created equal in this regard, or if some alder patches are better positioned to provide these subsidies.
l. 1987-2001: There is more literature on this issue that you m ight consider incorporating here. Triska et al. (2007) did a nice study on the transport and transformation of nitrogen as it moved from a hillslope to a headwater riparian wetland and into and down the headwater st ream, with the latter being pertinent in this case. Also, Hill and Lymburner (1998) and Hill et al. (1998) di d nice studies on nitrogen transformations in hyporheic zones, showing that even short, shallow, and fast f lowpaths through the hyporheic zone areMark C. Rains, Ph.D.

A-69 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE sufficient to transform a large amount of the availabl e nitrogen. These studies are all nice compliments to Alexander et al. (2000), which is already described in the docu ment.
l.2035-2047: I’ve always thought of spiraling as a form of short- and long-term storage. Nutrients are essential, yet are always in motion toward the receiving water bodies (e.g., the ocean). Nutrient spiraling is a way by which those nutrients are temporarily stored, per haps for a short time (e.g., algae), or perhaps for a long-time (e.g., trees), before being released again to downstream ecosystems. This is similar to the roles played by woody debris and floodplains in the short- and long-term storage of sediments.
l. 2398-2407: You make a good argument, but you might consider adding the importance of upstream migration. I don’t know much about this, but I’m led to believe t hat invertebrates tend to fly upstream after emergence, all the better to recolonize upstream habitats that tend toward depopulation due to drift. I don’t know if this actually true—though it seems that it must be true— or of there is any literature on this if it is true—though I do recall being told that there is literature on this by someone knowledgeable.
l. 2486-2487: You might consider adding a paragraph here on the impo rtance of anadramous fish in transporting nutrients, especially marine-derived nutrien ts, to headwater streams and associated riparian habitats. There is a good review of this in Nadeau and Ra ins (2007).
l. 2486-2487: You might also consider adding a paragraph here on bar riers and the effects of barriers. Dynesius and Nilsson (1994) showed that 77% of the total water discharge of the 139 largest river systems in North America north of Mexico, Europe, and the former S oviet Union are fragmented by dams and/or significant water abstraction. Stanford et al. (1988), War d and Stanford (1995), and Stanford and Ward (2001) talked about this in terms of the natural flow of mass, e nergy, and organisms, terming the overall effect the Serial Discontinuity Concept. And Fleckenstein et al. (2004) provided a good example of this, by showing that groundwater pumping causes a regional groundwater drawdown, which causes enhanced groundwater recharge through the streambed of the Cosumnes River, which causes the cessation of flow in Cosumnes River in the early fall, which creates a barrier to a fall-run Chinook salmon population.

2. This report concludes that open water and wetlands in riparian areas and floodplains of streams and rivers are physically, chemically, and biologically connect ed with the river network, and that their functions exert a strong influence on the char acter and functioning of downstream waters.
a) Are these conclusions supported by the scientific evidence? b) Does the report include the most relevant peer-revie wed literature on these topics, including evidence of connectivity and isolation? If not please indicate which references a re missing.
c) Was the reviewed literature cited and summarized cor rectly? If not please indicate where correction or revision is needed.

SUMMARY The conclusions are supported by the scientific evidence provided . This is still a relatively easy task for the authors, because hydrological and ecological connectivity are funda mental tenets for these systems. However, I do have comments regarding some flaws and/or inadequacies in the scientific evidence provided asMark C. Rains, Ph.D.

A-70 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE justification. (See, also, the detailed comments related to the conceptual framework in the section titled “Additional Reviewer Comments” below.)

DETAILED COMMENTS
General Comment: The classification scheme used in this doc ument is unusual. I understand why you might want to separate this into channels, wetlands on floodplain s, and wetlands not on floodplains, given the regulatory environment. However, this is not a common way to c lassify wetlands, which makes the document a bit hard to follow. I think that you can leave this genera l separation in place, but you might then explain what kinds of wetlands might be included, using an HGM c lassification scheme. In this way, you can explain that this chapter is dealing with all kinds of wetlands—r iverine as well as flat, depressional, slope, lacustrine, and estuarine—as long as they are subject to regular or epi sodic flooding and therefore connection to streams.
l. 3524-3556: This entire section would be greatly strengthened if you would include a review of some of the papers that show that hydrological and ecological connectivity a re central tenets of floodplain hydrology and ecology. Some examples might include the Flood Pulse Concept ( Junk et al., 1989, Tockner et al., 2000) and the extension of the Serial Discontinuity Concept to floodplain s (Ward and Stanford 1995). Doing so will accomplish two objectives: (1) make it clear from the outs et that we’ve long since accepted hydrological and ecological connectivity as fundamental tenets and (2) provide critical context for much of the remaining discussion of the specific examples.
l. 3574-3575: You might also consider adding a paragraph here on the role that bank storage plays in supporting baseflow, especially immediately following high flow s (Whiting and Pemeranets 1997, Hammersmark et al., 2008).
l. 3584-3585: Here and in a few other locations, you use the word “filter” to describe sediment removal from flowing water by riparian and floodplain wetlands. However, i t isn’t a filtering effect, it’s a hydraulic effect, as water slows, loses strength (e.g., specific stream power), and deposits sediments, usually in order of mass (Meyer et al., 1995, Dabney et al., 1995). You know this to be true, because you go on to say as much later (e.g., l. 3601-3602). This is a little issue; but you’ll forgive me because it’s a pet peeve of mine.
l. 3601: Riparian areas are both sources and sinks for sedime nts. Riparian areas provide both short- and longterm storage locations for sediments, and can be sedim ent neutral, sediment sinks, or sediment sources depending upon whether the stream has reached its base profile—i n which case sediment storage and mobilization balance; accommodation space has been created—i n which case, sediments can be stored; or accommodation space has been destroyed—in which case, sediment s can be mobilized (Quirk 1996).
l. 3609-3618: This paragraph seems out of place, in that it does n’t seem to connect to the surrounding discussion of connectivity, but it will fit much better if you br oaden the previous paragraph as suggested in my comment titled “l. 3601”.
l. 3644-3646: Groundwater does not always move through the alluvium and /or equilibrate with the temperature of alluvium. Some groundwater that discharge s to riparian environments flows along regionalMark C. Rains, Ph.D.

A-71 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE groundwater flowpaths, and is therefore more likely to ha ve the temperature of the volumetric weighted average of the recharge water (Rains and Mount 2002, Kish et al., 2010).
l. 3695-3697: This paper, and a few others, have created a lot of headaches in recent years, because of sentences just like this, which imply that evapotranspira tion causes water levels to rise. The paper, in my opinion, is a bit flawed, in that it misrepresents the ne t effect of evapotranspiration and makes a claim wholly unsubstantiated by the data. Let me deal with these issues on at a time. First, evapotranspiration causes a net decline in water levels, which will tend to move water out of the carbon-rich soils. Hydraulic lift does occur, but that only partially offsets the initial drawdown. Imagine a point just below the water table but in the carbon-rich soils. Before evapotranspiration, that point is saturated, so the pressure potential is positive. Afte r evapotranspiration, the water table declines to below that po int, so the point is unsaturated, so the pressure potential is negative. At this point, water can flow uphill, down the pressure gradient, from the water table up toward the point. (This, in fact, is the source of the wel l-known capillary fringe.) The point may not be saturated—in fact, in most alluvial deposits, the point w ill not be saturated—though it likely will be moister than in the absence of the hydraulic lift. Still, the net eff ect, for this point, is that it went from saturated to unsaturated, which means that less water, not more wat er, is in the carbon-rich soils. Second, this means tha t less, not more, N transformations are likely to occur. More importantly, Kellogg et al. (2008) wasn’t about N transformations at all—this was just a purely speculative paragraph based upon no data that, quite frankly, the editors and reviewers at JAWRA should have asked to be rem oved.
l. 3702-3705: What do you mean by “redoxing agents”?
l. 3708-3734: This entire section is poorly referenced. This is nitrogen in riparian and floodplain wetlands, for which there are many studies, and yet only one study is referenc ed. Granted, the paper is good, and well referenced itself, but it seems like you, too, could bolst er your argument with additional references, such as the roles played by riparian wetlands in reducing nitrogen loa ds in agricultural runoff (Peterjohn and Correll 1984), the roles played by hyporheic flows, including those at t he channel-floodplain interface, in reducing nitrogen in stream waters (Dahm et al., 1998, HIill and L ymburner 1998, Hill et al., 1998), and the role that linked hillslopes-headwater wetlands-headwater streams play in reducing nitrogen loads as water flows from hillslopes to river networks (Triska et al., 2007).

l. 3835-3836: Add Tockner et al. (2000) to the references here. Junk e t al. (1989) developed the flood-pulse concept for tropical rivers; Tockner et al. (2000) extended the fl ood-pulse concept to temperate rivers.Mark C. Rains, Ph.D.

A-72 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE 3. This report concludes that for non-riparian/non-flood plain wetlands that are not connected to the river network through a stream channel (i.e., geographical ly isolated wetlands and wetlands that spill into losing streams), connectivity and isolation vary wit hin a watershed and over time, making it difficult to generalize about their connections to, or isolation from, downstream waters. The literature we reviewed does not provide sufficient infor mation to evaluate the degree of connectivity (absolute or relative) of these non-riparian particular w etlands.
a) Are these conclusions supported by the scientific evidence? b) Does the report include the most relevant peer-revie wed literature on these topics, including evidence of connectivity and isolation? If not please indicate which references a re missing.
b) Was the reviewed literature cited and summarized cor rectly? If not please indicate where correction or revision is needed.

SUMMARY The conclusions are supported by the scientific evidence provided . This is the most difficult task for the authors, because hydrological and ecological connectivity are not fundamental tenets for these systems. However, I do have comments regarding some flaws and/or inadeq uacies in the scientific evidence provided as justification and regarding the wording of the conclusion , which I think soft-peddles the conclusion. (See, also, the detailed comments related to the conceptual frame work in the section titled “Additional Reviewer Comments” below.)

DETAILED COMMENTS l. 4004-4017: This is a confusing paragraph. At first, it seems like only depressional wetlands are going to be included, and it’s not until l. 4008 and beyond that other typ es of wetlands are mentioned. I suggest listing all of the types as a list in the first sentence, then cla rifying the details in order thereafter.
l. 4025-4098: You might consider wind transported snow as a special case of hydrological connectivity. In that regard, you might consider including Rains (2011), who showed t hat moraine, ice-scour, and dead-ice depressional wetlands serve as groundwater recharge focal po ints because aeolian-transported snow is trapped in the topographic lows in winter and then melts and rec harges underlying groundwater immediately following breakup in late spring, with the net effect being th at groundwater recharge rates in these depressional wetlands is 37%-332% of the broader surrounding landsc ape.
l. 4053-4078: You might also consider discussing the special but very i mportant case of groundwater flowthrough wetlands. Groundwater flow-through lakes and depression al wetlands, where surface waters are a surface expression of broader groundwater phenomena, have long be en recognized. Born et al. (1979) and Rains (2011) described groundwater flow-though depressional we tlands in glaciated landscapes, Sloan (1972) and Richardson et al. (1992) described groundwater flow-thr ough prairie potholes in the northern prairie, and Murphy et al. (2008) described groundwater flow-through depressi onal wetlands in clay-rich soils with abundant dessication cracks and other macropores. Rains et al. (2006) showed that vernal pools in central California are a special case, being groundwater flow-thou gh wetlands supported by a seasonal perched aquifer that is unconnected to the underlying regional aquifers

.Mark C. Rains, Ph.D.

A-73 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE l. 4100-4116: You might consider explaining why depressional wetlands are so good at storing surface water. Though water can be stored in uplands, too, surface-water storage in wetlands is more efficient than shallow groundwater storage in uplands, because wetlands have an eff ective specific yield of ~1.0 (i.e., the entire empty portion of the basin is available for storage) in m ost circumstances (Sumner 2007), while upland deposits have a specific yield of ~0.1-0.2 (i.e., only 10-20% of the deposits are voids available for storage) in most circumstances (Johnson 1967).
l. 4145-4146: Hammersmark et al. (2008) showed that this dry-seas on baseflow ceased earlier when an incised river was restored to the historic floodplain. O ne of the reasons for this was that evapotranspiration was higher in the restored floodplain wetlands than in the previously drier floodplain uplands.

l. 4390-4398: This is the first occurrence of this list, which recurs a few times hereafter. In all cases, you should add that wetlands can be connected by groundwater connec tions to one another and to nearby streams.
l. 4401-4402, l. 4415-4425: I lump these specific lines together in one com ment to make an important point. In the first case, you state in clear, concise, and u nequivocal terms that riparian and floodplain wetlands are highly connected to river systems. In the second case, you dit her for a few paragraphs, then finally get around to saying that non-riparian and channel origin wetlands m ight be connected to river systems under certain circumstances. You are correct; however, by dithering and the n only vaguely supporting the idea that nonriparian and channel origin wetlands might be connected to ri ver systems, and then only under certain circumstances, I think that you soft-peddle what we know abo ut the flow of water across landscapes. To be honest, all hydrologic systems are interconnected to some degre e or another—that’s why hydrologists refer to the entire water cycle environment as the hydrosphere. All we’re really debating here is the degree to which non-riparian and channel origin wetlands are connected to river systems. There is no bright line between connected and isolated, there is only a vague gray area wher e we might choose to transition from their being a significant nexus to their not being a significant nexus. This w as a central point to the arguments by Nadeau and Rains (2007), and I think it’s an important argument to make here, because the scientific evidence clearly supports that position.
l. 5295-5298: Vernal pools aren’t really located in what most peo ple in the West would consider “coastal areas of the western United States”. For example, Rains et a l. (2006, 2008) were working in the Central Valley of California, in vernal pools that were 2-3 hours drive from the coast. I think it more correct to just say “the western United States” or “Mediterranean-like climates in the western United States”.
l. 5314-5318: You might consider adding Rains et al. (2006) to the r eferences at the end of this sentence.
l. 5385-5387: You might consider adding Rains et al. (2006) to the r eferences at the end of this sentence.
l. 5401-5412: There is a key difference between these two typ es of vernal pools that you have missed. The vernal pools on clay-rich soils are perched surface-water s ystems; the vernal pools on hardpan soils are perched surface-water and groundwater systems. This makes them behave very differently from a hydrological perspective.
Table 5-2, Table 5-3: These tables provide are concise synthesis. Can one be made for rivers?Mark C. Rains, Ph.D.

A-74 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE 4. This report concludes that while the influence of a particular stream or wetland on downstream waters might be small, the aggregate contribution by an entire class of streams or wetlands (e.g., all ephemeral streams in the river network, or a cluster of small wetlands) might be substantial.
a) Is this conclusion supported by the scientific evi dence? b) Does the report include the most relevant peer-revie wed literature on this topic? If not please indicate which references are missing.
c) Was the reviewed literature cited and summarized cor rectly? If not please indicate where correction or revision is needed.

SUMMARY To be honest, I don’t see where you make this case explicitly at all. I do think that it is true, or at least that it can be true. For example, there’s no doubt that obliterating a single headwater stream high up in the watershed will have no measurable effect on the large, mainstem river where it discharges to the ocean, but there’s equally no doubt that obliterating all of the headwater stre ams in the watershed will have a measurable and catastrophic effect on the large, mainstem river where it discharges to the ocean. Justice Kennedy, in his opinion in Rapanos v U.S. (2006), would seem to agree. I do think that the basic piece s are in this document to make that case, but I think it important that you expl icitly make this case, both throughout the document (e.g., in a paragraph or section when discussing streams , riparian and floodplain wetlands, and non-riparian and channel origin wetlands) and in a single standalone sec tion, perhaps referencing the voluminous cumulative effects literature (e.g., Bedford and Prest on 1988, Lee and Gosselink 1988, Childers and Gosselink 1990, Johnston 1994, and many others). The latter could be done toward the end of the conceptual model, after you have shown landscape-scale connectivity betwee n all of the disparate pieces separately discussed in this document. The former could then be done wit h examples within the individual discussions of the disparate pieces discussed in this document. You already do some of this—for example, you do discuss the role that depressional wetlands play in storing water an d reducing stormflows (l. 4100-4116)—but you probably should do more and more explicitly state the point th at you are trying to make here whenever you do.
There are numerous examples of this with regards to fl ood storage that you could add to those that you already have discussed. Non-floodplain wetlands temporarily store surface water, thereby attenuating and translating flood peaks in downstream river networks (Haan and Johnson 1968, Hubbard and Linder 1986). This phenomenon is so well known that rainfall-runoff models ty pically have a step when a storm begins where rainfall is abstracted and put into depressional stor age and is unavailable for runoff throughout the remaining storm (McCuen 2005). However, storage capacity is a finite quantity that can be exceeded, suggesting that flat and depressional wetlands will have the greatest effect during smaller storms (Haan and Johnson 1968). In fact, ephemeral surface-water connections occurr ing immediately following larger storms are an indication that storage capacity has been exceeded and subsequent water is immediately discharged (Rains et al., 2006, Rains et al., 2008).
There are also implicit examples of both flood storage an d other processes that can be inferred from the literature. Depressional wetlands can focus groundwater r echarge. As described elsewhere, Rains (2011) showed this to be the case for moraine, ice-scour, and dead -ice depression in southwest Alaska. He did notMark C. Rains, Ph.D.

A-75 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE specifically upscale—necessary spatial data were lacking—but he did show that these types of wetlands are perhaps the most numerous and conspicuous types of wetland s in these environments, implying that, though the individual effect of one wetland may be negligible, the cum ulative effect of the many thousands of wetlands must necessarily be important. In this case, t he effect is implicit, not explicit, but you could nevertheless make this point more strongly by explicitly stating this implicit assumption.

ADDITIONAL LITERATURE CITED (i.e., literature cited in this review not already cited in the document)
Bedford, B.L., and E.M. Preston. 1988. Developing the scie ntific basis for assessing cumulative effects of wetland loss and degradation on landscape functions: Status, perspectives, and prospects. Environmental Management 12:751-771.
Born, S.M., S.A. Smith, and D.A. Stephenson. 1979. The hyd rologic regime of glacial terrain lakes. Journal of Hydrology 43:7–44. Bull, W.B. 1991. Geomorphic Response to Climate Change. Oxfo rd University Press, New York.
Childers, D.L., and J.G. Gosselink. 1990. Assessment of cu mulative impacts to water quality in a forested wetland landscape. Journal of Environmental Quality 19:455–464. Dabney, S.M., L.D. Meyer, W.C. Harmon, C.V. Alonso, and G.R. Foster. 1995. Depositional patterns of sediment trapped by grass hedges. Transactions of the Ameri can Society of Agricultural Engineers 38:1719–1729.
Dynesius, M., and C. Nilsson. 1994. Fragmentation and flow regu lation of river systems in the northern third of the world. Science 266:753–762.
Fleckenstein, J., M. Anderson, G. Fogg, and J. Mount. 2004. M anaging surface water-groundwater to restore fall flows in the Cosumnes River. Journal of Water Resour ces Planning and Management 130:301–310.
Freeman, M.C., C.M. Pringle, and C.R. Jackson. 2007. Hydrolog ic connectivity and the contribution of stream headwaters to ecological integrity at regional sca les. Journal of the American Water Resources Association 43:5–14.
Kish, G.R., C.E. Stringer, M.T. Stewart, M.C. Rains, and A.E. Torres. 2010. A geochemical mass-balance method for base-flow separation, upper Hillsborough River wa tershed, west-central Florida, 2003-2005 and 2009. U.S. Geological Survey Scientific Investigations Repo rt 2010–5092. U.S. Government Printing Office, Washington, DC. Haitjema, H.M., and S. Mitchell-Bruker. 2005. Are water t ables a subdued replica of the topography? Ground Water 43:781–786.
Hammersmark, C.T., M.C. Rains, and J.F. Mount. 2008. Qu antifying the hydrologic effects of stream restoration in a montane meadow environment. River Research a nd Applications 24:735–753.
Haan, C.T., and H.P. Johnson. 1968. Hydraulic model of runoff from depressional areas, I: General considerations. Transactions of the American Society of A gricultural Engineers 11:364–367.Mark C. Rains, Ph.D.

A-76 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE Hill, A.R. and D.J. Lymburner. 1998. Hyporheic zone chemistry a nd stream-subsurface exchange in two groundwater-fed streams. Canadian Journal of Fisheries and Aquatic Sciences 55:495–506. Hill, A.R., C.F. Labadia, and K. Sanmugadas. 1998. Hyporhei c zone hydrology and nitrogen dynamics in relation to the streambed topography of a N-rich stream . Biogeochemistry 42:285–310.
Holloway, J.M., and R.A. Dahlgren. 2001. Seasonal and event -scale variations in solute chemistry for four Sierra Nevada catchments. Journal of Hydrology 250:106–121.
Hubbard, D.E., and R.L. Linder. 1986. Spring runoff retention in prairie pothole wetlands. Journal of Soil and Water Conservation 41:122–125.
Johnson, A.I. 1967. Specific yield - compilation of specific yie lds for various materials. U.S. Geological Survey Water-Supply Paper 1662-D. U.S. Government Printing Offic e, Washington, DC. Johnston, C.A. 1994. Cumulative impacts to wetlands. Wetlands 14: 49–55.
Lee, L.C., and J.G. Gosselink. 1988. Cumulative impacts on w etlands: Linking scientific assessments and regulatory alternatives. Environmental Management 12:591–602.
Mahoney, J.M., and S.B. Rood. 1998. Streamflow requirements for cottonwood seedling recruitment—an integrative model. Wetlands 18:634–645.
McBride, J.R., and J. Strahan. 1984. Establishment and surv ival of woody riparian species on gravel bars of an intermittent stream. American Midland Naturalist 112:235–245. McCuen, R.H. 2005. Hydrologic analysis and design, 3/E. Prenti ce-Hall, Upper Saddle River, New Jersey. Meyer, L.D., S.M. Dabney, and W.C. Harmon. 1995. Sediment-tr apping effectiveness of stiff-grass hedges. Transactions of the American Society of Agricultural Engi neers 38:809–815. Murphy, K.E., M.C. Rains, M.G. Kittridge, M. Stewart, a nd M.A. Ross. 2008. Hydrological connectivity between clay settling areas and surrounding hydrological lands capes in the phosphate mining district, peninsular Florida, USA. Journal of the American Water Re sources Association 44:980–995.
Nadeau, T.L., and M.C. Rains. 2007. Contribution of headwaters to downstream integrity: Introduction to the JAWRA special issue. Journal of the American Water Res ources Association 43:1–4. Parenteau, P. 2004-2005. Bad calls: how Corps' Districts are m aking up their own rules of jurisdiction under the Clean Water Act. Vermont Journal of Environmental Law 6. http://www.vjel.org/journal/VJEL10019.html

. Peterjohn, W.T., and D.L. Correll. 1984. Nutrient dynamics i n an agricultural watershed: observations on the role of a riparian forest. Ecology 65:1466–1475.
Pringle, C.M. 2001. Hydrologic connectivity and the management o f biological reserves: a global perspective. Ecological Applications 11:981–998.
Pringle, C.M. 2003a. The need for a more predictive understanding of hydrologic connectivity. Aquatic Conservation 13:467–471.Mark C. Rains, Ph.D.

A-77 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE Pringle, C.M. 2003b. What is hydrologic connectivity and why is i t ecologically important? Hydrological Processes 17:2685–2689. Rains, M.C. 2011. Water sources and hydrodynamics of closed-ba sin depressions, Cook Inlet Region, Alaska. Wetlands 31:377–387.
Rains, M.C., and J.F. Mount. 2002. Origin of shallow ground w ater in an alluvial aquifer as determined by isotopic and chemical procedures. Ground Water 40:552–563.
Richardson, J.L., L.P. Wilding, and R.B. Daniels. 1992. Recharge and discharge of groundwater in aquic conditions illustrated with flownet analysis. Geoderma 53:65–78.
Scott, M.L., J.M. Friedman, and G.T. Auble. 1996. Fluvial pro cess and the establishment of bottomland trees. Geomorphology 14:327–339.
Shaftel, R., R. King, and J. Back. 2012. Alder cover drives nitrogen availability in Kenai lowland headwater streams, Alaska. Biogeochemistry 107:135–148.
Sinclair, W.C. 1977. Experimental Study of artificial rec harge possibilities in northwest Hillsborough County, Florida. U.S. Geological Survey Water-Resources Investigat ions 77-13. U.S. Geological Survey, Tallahassee, Florida.
Sloan, C.E. 1972. Ground-water hydrology of prairie potholes i n North Dakota. U.S. Geological Survey Professional Paper 585-C. U.S. Government Printing Office , Washington.
Stanford, J.A., F.R. Hauer and J.V. Ward. 1988. Serial discontinuity in a large river system. Verh. Internat. Verein. Limnol. 23:111–1118.
Stanford, J.A. and J.V. Ward. 2001. Revisiting the serial discontinuity concept. Regulated Rivers: Research and Management 17:303–310.
Sumner, D.M. 2007. Effects of capillarity and microtopograph y on wetland specific yield. Wetlands 27:693– 701. Tate, K.W., R.A. Dahlgren, M.J. Singer, B. Allen-Diaz, and E.R. Atwill. 1999. Timing, frequency of sampling affect accuracy of water-quality monitoring. Cali fornia Agriculture 53:44–48.
Tihansky, A.B. 1999. Sinkholes, west-central Florida. Pp. 121-140 in D. Galloway, D.R. Jones, and S.E. Ingebritsen (eds.), Land subsidence in the United States. U. S. Geological Survey Circular 1182. U.S. Government Printing Office, Washington, DC.
Tockner, K., F. Malard, and J. V. Ward. 2000. An extension of the flood pulse concept. Hydrological Processes 14:2861–2883.
Toth, J. 1963. A theoretical analysis of groundwater flo w in small drainage basins. Pp. 75–96 in Proceedings of Hydrology Symposium No. 3, Groundwater, Queen’s Printer, Ottawa, Canada. Triska, F.J., J.H. Duff, R.W. Sheibley, A.P. Jackman, and R.J. Avanzino. 2007. DIN retention-transport through four hydrologically connected zones in a headwater catchm ent of the upper Mississippi River. Journal of the American Water Resources Association 43:60–71.Mark C. Rains, Ph.D.

A-78 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE Ward, J.V. and J.A. Stanford. 1995. The serial discontin uity concept: extending the model to floodplain rivers. Regulated Rivers: Research and Management 10:159–168. Wolman, M.G., and J.P. Miller. 1960. Magnitude and freque ncy of forces in geomorphic processes. Journal of Geology 68:54–74.A-79 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE



### John S. Richardson, Ph.D.

Professor Department of Forest Science University of British Columbia Vancouver, BC, Canada

Dr. John Richardson is a professor at the University of British Columbia in the Department of Forest Sciences. In addition to over 150 publications and more than 30 graduate students completed, he serves on editorial boards of two international journals and 2 endange red species recovery teams. His research on the effects of forestry and other land-uses on freshwater an d riparian ecosystems is recognized internationally. He teaches about aquatic and riparian ecosystems, and the organisms they sustain. More on his work can be found at http://faculty.forestry.ubc.ca/richardson/John S. Richardson, Ph.D.

A-81 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE 

### Peer Review Meeting of EPA’s Draft Report: Connectivity of Streams and Wetlands to Downstream Waters – A Review and Synthesis of the Scientif ic Evidence

Comments submitted by Dr. John S. Richardson

GENERAL COMMENTS (Technical charge comments below)

This is a very nicely written and comprehensive document . The regulatory context is explained very well as background to understanding the intent of the report. The defi nitions of terms such as riparian, wetland, connection, etc., are given so that the details are explicit . The case studies approach to giving explicit examples and how their connections would be interpreted is a good idea and very effective, especially given that the examples were for systems that could be quest ioned about their connectedness with navigable waters, depending upon interpretation of the terms of the legal opinions . The figures are effective in illustrating principles and evidence.
The conceptual framework with source, sink, lag, transfo rmation and refuge (Leibowitz et al., 2008) is a nice idea, and it provides a good way to educate readers about the kinds of processes, and how they are influenced by spatial scales and temporal scales. However, this fr amework doesn’t seem to be used throughout the stream examples (chapter 4). For instance, the example from the pr airie streams doesn’t mention these conceptual components much. The examples given about streams provide good exampl es demonstrating the processes that connect the small tributaries to downstream reaches, but it would be useful to better link these with the conceptual framework. The wetland chapter (5) does a better job of bringing these model terms into the description throughout that section.
A “non-riparian” wetland (NRCWs – non-riparian and channel origin wetlands) seems an odd term, but I wonder if non-floodplain wetland might be better? The definit ion of riparian area as transitional between aquatic and terrestrial (P.26) makes it difficult to know w hen one might no longer be in transition across a floodplain, for example. Gregory et al.’s (1991) definition of riparian area would make it difficult to have a non-riparian wetland, unless this simply means not in the r iparian area of a navigable-in-principle stream. The consistent use of floodplain and riparian as a combination te rm (e.g., L.590) makes me think that floodplain might be sufficient (later in Chapter 5 the use of “ripar ian/floodplain” makes them seem interchangeable). Chapter 5 appeared confusing as to whether wetlands were flood plain/riparian (P.212) or NRCWs at some points, but maybe these were to apply to all wetlands. At one point (L. 594) it says that both floodplain and NRCWs could be geographically isolated, but I am having diffic ulty seeing how this definition of surrounded by uplands could apply to floodplain wetlands.
It seems like the methylation of mercury is better explaine d on P.233 than it is earlier in the chapter when mercury is discussed for NRCWs. Perhaps the explanation co uld be moved up to provide the detail when it is first mentioned.
Coastal streams entering the oceans, and not a naviga ble-in-principle river, might not be covered under the definitions used in this report.John S. Richardson, Ph.D.

A-82 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE Some sections seem to convey a lot of information that is somewhat peripheral to the issue at hand, for instance, it is not clear what the material on P.136-137 con tributes to the understanding of whether this is a navigable-in-principle stream or tributary to a navigable -in-principle stream.

It wasn’t clear what the distinction between Carolin a Bays and Delmarva Bays is, or whether it is solely geographic. The Glossary did not help with that.
It appeared to me that the Executive Summary was a littl e long, depending upon who the anticipated audience for this might be. There is a lot of territory to cover, and perhaps the regulators will need this much information. The summary is sound, so I am not criticiz ing the content, just the length.
I am still a bit vague on the opinion of the other 4 justices that were not included in the Scalia or Kennedy statements. I think that the other opinion(s) should be explained a little further.
I like the idea of proportional benefits from non-navigable wa ters, as expressed in the Leibowitz et al. (2008) paper. Moreover, the idea that these benefits may be reali zed or potential benefits is a helpful way to think about the capacity of a source system to provide benefit. H owever, these benefits may not be linear with respect to concentration or rates in their contributions. For instance, some nitrogen released to downstream would be beneficial, whereas too much would be detrimenta l, and the relative benefit might vary in a way that not add up so nicely.
Some authors, such as Stan Gregory (Oregon State U), are t rying to discourage the use of “large woody debris” (L.1780), and in preference use “large wood” to avoid connotations of waste material given what we know about the important geomorphic and cover roles of large wood in streams and wetlands.
The “Draft guidance ...” document appears to be for field s taff, and perhaps a decision tree or flow diagram might be useful to distinguish classes of entities and then refer from that to detailed guidance. It seems like a hefty document to plow through to determine what kind of sy stem they are looking at. Of course, all the document is needed, but some way to sort through it quickly m ight be helpful.

Editorial
L.3135 – change “particularly” to “particular”
L.4929 – family Chironomidae, not subfamilyJohn S. Richardson, Ph.D.

A-83 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE TECHNICAL CHARGE QUESTIONS

1. This report concludes that all streams, regardless of f low duration or size, are physically, chemically, and biologically connected to rivers; and these connections, individually or cumulatively, exert a strong influence on the character an d functioning of downstream waters.

a) Are these conclusions supported by the scientific evid ence?
Yes, the conclusions are consistent with the evidence presen ted in the scientific, peer-reviewed literature.

a) Does the report include the most relevant peer-reviewed literature on these topics, including evidence of connectivity and isolation? If not please indicate which references are missing.
The authors provide a comprehensive suite of references to support their summary and conclusions. These references are the most relevant, and other papers that come to mind would not further enhance the understanding of the topic. One that deals with the punctuated del ivery of large wood to channels and its storage and lag processes is by Swanson et al. (1998).

Swanson, F.J. et al. 1998. Flood disturbance in a forested mountain landscape - Interactions of land use and floods. BioScience 48:681-689.

b) Was the reviewed literature cited and summarized correc tly? If not please indicate where correction or revision is needed.
The review provides a solid assessment of the literature a nd covers the evidence for connections. Yes, the conclusions are supported and appropriate literature is compil ed. The authors have been careful throughout to point out any uncertainties in the conclusions that can be drawn from the available literature. The only limitation to the assertion that all streams are connected to rivers might be in the case of coastal streams not contributing to a nexus with a navig able-in-fact river, but these are still connected to streams (or estuaries) downstream.

2. This report concludes that open water and wetlands in riparian areas and floodplains of streams and rivers are physically, chemically, and biologically connect ed with the river network, and that their functions exert a strong influence on the char acter and functioning of downstream waters.

a) Are these conclusions supported by the scientific evid ence?
This provides a very good summary of the literature and the conclusions are supported.

b) Does the report include the most relevant peer-reviewed literature on these topics, including evidence of connectivity and isolation? If not please indicate which references are missing.

The literature covered is excellent.John S. Richardson, Ph.D.

A-84 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE c) Was the reviewed literature cited and summarized correc tly? If not please indicate where correction or revision is needed.
The interpretations of what is known and the limitations of inferences possible from the literature are fine. The authors do a very good job throughout the document of ensur ing they point out the uncertainties in demonstrating significant connections. Good examples given to des cribe the types of wetlands and their connections to navigable rivers.
I find the use of the term riparian a little confusing. It would be hard to distinguish functionally or structurally in most cases how a floodplain differed from a riparian area, so to refer to “riparian and floodplain” wetlands seems redundant (see definition of ripari an on P.26). This also goes to whether there is such a thing as a non-riparian wetland, as a wetland should generate its own riparian area. Perhaps this should be defined as a non-floodplain wetland.

3. This report concludes that for non-riparian/non-flood plain wetlands that are not connected to the river network through a stream channel (i.e., geographical ly isolated wetlands and wetlands that spill into losing streams), connectivity and isolation vary wit hin a watershed and over time, making it difficult to generalize about their connections to, or isolation from, downstream waters. The literature we reviewed does not provide sufficient infor mation to evaluate the degree of connectivity (absolute or relative) of these non-riparian particular w etlands.

a) Are these conclusions supported by the scientific evid ence?
The conclusions are supported and carefully reviewed. The connection is supported for some cases, but not for all, so I agree that one cannot categorically c onclude that this class of wetlands is connected. The role of isolated wetlands in storing water that may re duce runoff intensity and storm-flow generation to streams is a good idea that deserves further study to empiri cally back up the simulations presented. Likewise, the contributions of these isolated wetlands on tr ansformation and storage of nutrients, thereby preventing their transport to rivers could be another import ant mechanism by which these wetlands contribute to navigable rivers and deserves field trials. The uncertainties associated with the connections of non-floodplain wetlands are carefully acknowledged for the examples, especially for the example of coastal bays, which have some indications of connections, but not strong, and the authors are careful to address that. The prairie potholes likewise occupy a conti nuum, but most have evidence of some connection. The distinction made to clarify geographic isolat ion from functional connectivity is useful.

b) Does the report include the most relevant peer-reviewed literature on these topics, including evidence of connectivity and isolation? If not please indicate which references are missing.
The literature reviewed is excellent and represents sta te-of-the-science.John S. Richardson, Ph.D.

A-85 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE c) Was the reviewed literature cited and summarized correc tly? If not please indicate where correction or revision is needed.
The summary of the literature is very good and the authors ha ve appropriately represented the collective evidence.

4. This report concludes that while the influence of a particular stream or wetland on downstream waters might be small, the aggregate contribution by an entire class of streams or wetlands (e.g., all ephemeral streams in the river network, or a cluster of small wetlands) might be substantial.

a) Is this conclusion supported by the scientific eviden ce?
Given the preponderance of small streams and wetlands that are not navigable in and of themselves, they in aggregate do contribute enormously to navigable systems . The conclusions drawn by the authors are sound and well supported by the literature.

b) Does the report include the most relevant peer-reviewed literature on this topic? If not please indicate which references are missing.
The review has covered a comprehensive set of literature r elevant to the topic.

c) Was the reviewed literature cited and summarized correc tly? If not please indicate where correction or revision is needed.
The authors have made a very thorough search of the literat ure for appropriate references and have drawn appropriate conclusions, including pointing out any uncertainti es about the conclusions possible.

Post-meeting comments It seems that there is a need to go beyond connectivity, to include aspects of the effects downstream. This was made clearer during the meeting. It also clarified why the re were sections of the charge questions that seemed more about the aggregate effects downstream, particularly question #4. This topic is not well covered in the report, and a separate section on downstream effects woul d be warranted. The connectivity aspects do not try to address the magnitudes of effect sizes. Along with the discussion of effects, the nature of those effects, and especially cumulative effects, needs to be elaborated. After the fact, I realized that the title “Connectivit y...” in the report and all the workshop documentation led me to focus on the connections and not the effects. Given that the 1 st , 2 nd

and 4 th charge questions seem to be about consequences downstream, perhaps that should be better reflected in the title. It would cert ainly have drawn our attention more specifically to the quantification of effects.
As discussed in the meeting on the 30 th January, the confusion over floodplain versus riparian needs to be clarified. Likewise, the category of non-floodplain wet lands needs more refinement as it covers an enormous range of wetland types. I think that if “floodplain” equa ls “riparian” in this scheme, then the use of floodplain should suffice. I found the use of “riparian” was not in li ne with what I consider to be riparian, but then it needs defining either way.John S. Richardson, Ph.D.

A-86 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE The executive summary needs to be shortened. As currently written it is rather long. I cannot determine who would read such a long summary. I know the document is inte nded for a broad readership, but perhaps a single page for the executive summary, and then the synthesis in the end of the document might cover all the rest of what is currently in the executive summary.
A brief section outlining uncertainties would be helpful. Pe rhaps that could go into an expanded chapter 6. This could provide a useful focal point for research to be done, or simply to provide an alert as to what we have less confidence in saying as a scientific community. It is reasonable to acknowledge that there remain uncertainties around the science.
The final section should be a synthesis and have some decl arative statements, such as are included in the charge questions. The current 6 pages of chapter 6 seems i nsufficient compared to the enormous detail of the remainder of the document.

Here are some additional references, from those that addr ess spatially structured populations of amphibians in wetlands, to papers about effects from streams to estuarie s, resource subsidies, and large-scale transformations of carbon along freshwater networks. The Naiman et al. ( 2000) reference includes the curves from the FEMAT (1993) exercise showing how different functions link up ri parian areas with water.

Additional references :
Cole J. J., Y.T. Prairie, N. F. Caraco, W. H. McDowe ll, L. J. Tranvik, R. G. Striegl, C. M. Duarte, P. Kortelainen, J. A. Downing, J. J. Middelburg, J. Melack. 2007. Plumbing the global carbon cycle: Integrating inland waters into the terrestrial carbon budget

. Ecosystems 10: 171-184
Richardson, J.S., Y. Zhang & L.B. Marczak. 2010. Resource subsidies across the land-freshwater interface and responses in recipient communities. River Research and Applications 26:55-66.
Sakamaki, T., J.Y.T. Shum & J.S. Richardson. 2010. Waters hed effects on chemical properties of sediment and primary consumption in estuarine tidal flats: importa nce of watershed size and food selectivity by macrobenthos. Ecosystems 13:328-337.
Sakamaki, T. & J.S. Richardson. 2008. Retention, breakdown and biological utilisation of deciduous tree leaves in an estuarine tidal flat of southwestern Britis h Columbia, Canada. Canadian Journal of Fisheries and Aquatic Sciences 65:38-46.
Naiman, R.J., R.E. Bilby and P. Bisson. 2000. Riparian ecol ogy and management in the Pacific coastal rain forest. BioScience . 50:996-1011.
Werner E.E. et al., 2007. Turnover in an amphibian metacomm unity: the role of local and regional factors. Oikos 116:1713-1725 DOI: 10.1111/j.2007.0030-1299.16039.x Hecnar SJ and MCloskey RT. 1996. Regional dynamics and the s tatus of amphibians. Ecology 77:2091-2097 DOI: 10.2307/2265703A-87 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE



### Joel W. Snodgrass, Ph.D. Chair, Department of Biological Sciences

Towson University Towson, MD

Dr. Joel W. Snodgrass holds a B.S. in biology (Guilford Col lege), M.S. in zoology (University of Central Florida), and Ph.D. in ecology (University of Georgia). Following his Ph.D. work Dr. Snodgrass was a Postdoctoral Associate at Rutgers University before joini ng the faculty at Towson University in 1999. He is currently a Professor and Chairperson in the Department of Biological Science and previously co-directed the Master’s of Biology Program from 2002 until fall 2011. Dr. S nodgrass’ current research interests include quantification of patterns of aquatic habitat fragmentat ion and the effects of aquatic habitat fragmentation on the evolution and ecology of aquatic vertebrate populations. Dr. Snodgrass has published more than 60 papers and book chapters, including papers in Canadian Journal of Fisheries and Aquatic Sciences
, Conservation Biology
, Ecology
, Ecological Applications
, Journal of Animal Ecology
, Environmental Chemistry and Toxicology and Wetlands . Dr. Snodgrass currently serves on the editorial boards of Copeia and Wetlands

.Joel W. Snodgrass, Ph.D.

A-89 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE 

### Peer Review Meeting of EPA’s Draft Report: Connectivity of Streams and Wetlands to Downstream Waters – A Review and Synthesis of the Scientif ic Evidence

Comments submitted by Dr. Joel W. Snodgrass

1. This report concludes that all streams, regardless of f low duration or size, are physically, chemically, and biologically connected to rivers; and these connections, individually or cumulatively, exert a strong influence on the character an d functioning of downstream waters.

a) Are these conclusions supported by the scientific evidence?
Yes, the scientific evidence clearly indicates a signific ant influence of physical and biological processes in streams having a large influence on downstream rivers. Streams provide significant amounts of materials (including nutrients, pollutants, sediments, and water) and organisms and control their temporal dynamics and rates of delivery to river systems

. b) Does the report include the most relevant peer-revie wed literature on these topics, including evidence of connectivity and isolation? If not please i ndicate which references are missing.
Although the report is focused on influences that move from upstream to downstream (as is clearly stated in the report), some degree of isolation of headwat er streams is important for the biological integrity of these habitats. For example, some species of stream-side salamanders are headwater specialist, which are only found in large numbers in headw ater streams (Snodgrass et al., 2007; Peterman et al., 2009). Headwater specialists often have a daptations that allow them to cope with desiccating conditions that limited the development of predat or populations (Meyer et al., 2007). Many insects as well as other invertebrate taxa are also endem ic to headwater streams (e.g., Dieterich and Anderson, 2000; Fend and Brinkhurst, 2000; Fend and Gustafson, 2001). Th erefore, protection of the isolated nature of headwater streams is also an importa nt component of protecting the biodiversity associated with our nation’s waters. The authors do acknowl edge these ideas (see lines 906-907; 1020- 1022), but I feel they are also important for managers and policy maker to appreciate. If the main focus of the report is the emphasis of effects on downstream wat ers, then more detailed treatment of the influence of connectivity on upstream headwaters and wetland s may not be warranted.
Although not crucial to demonstrating the influence of headwa ter streams for downstream rivers, in the sake of being complete it is probably worth noting the role of beavers in the functioning and influence of headwaters on downstream rivers. Beavers can dam extens ive lengths of moderate to low gradient headwater streams (e.g., Snodgrass 1997), greatly altering their hydrology and geomorphology (Pollock et al., 2003; Butler and Malanson, 2005) and provide habitat for numerous organisms (e.g., Snodgrass and Meffe 1996; Stevens et al., 2006). These hydrological and geomo rphological changes have large impacts on ecosystem function (Naiman et al., 1996) includin g greatly increased rates of denitrification (Naiman et al., 1994). Additionally, beaver ponds can be areas of high rates of mercury methylation (Roy et al., 2009). These points relate to the idea of headwa ter streams being places of lag andJoel W. Snodgrass, Ph.D.

A-90 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE transformation. This material should be added as the wet lands that beavers form would fall into the floodplain/riparian category of wetlands.
When the authors discuss mapping issues for headwater stream s (lines 1519-1530) they should include the Brooks and Calhoun (2011) reference; they might even include some numbers from this publication. Specifically, Brooks and Calhoun (2011) estimate that 21% of 400.3 km of stream did not show up as blue lines on 1:25,000 scale USGS topographic maps. There is als o the issue of channels that were formed under past land use scenarios that currently do not ever hold flowing water. Although the definition of “stream” includes flowing water (lines 503-504) lat er the authors suggest that headwater stream originate at where “runoff is sufficiently concentr ated to erode a definable channel” (line 518). Some clarification should be included to make it clear t hat there are two components to a stream: flow at some time during the year and the formation of a channel.
On lines 3399 through 3413 the authors summarize the effects of al tered flow regimes on invasiveness of native communities. Meffe (1984) should probably be cited here as this is one of the original, if not the original, documentation of the influence of natural flow regimes on co-existence of native and introduced fish species. Additionally, the bullet on line 3434 should include the prevention and/or mitigation of the effects of invasion by introduced specie s. Again, this is a place to integrate the balance between lag and source and how their alteration can impact downstream rivers.

c) Was the reviewed literature cited and summarized cor rectly? If not please indicate where correction or revision is needed.
In general, the literature interpretation is correct and the literature cited extensive. I have only a few minor comments here. On lines 2412 through 2414 the authors suggest that most fishes utilizing headwaters can also be found further downstream and cite Ho ritz (1978). This may be true for more species poor assemblages, but in more species rich areas it is common to find species of fish confined to headwater streams. See discussion above for references. Thi s change should be made in the final document.

2. This report concludes that open water and wetlands in riparian areas and floodplains of streams and rivers are physically, chemically, and biologically connect ed with the river network, and that their functions exert a strong influence on the char acter and functioning of downstream waters.

a) Are these conclusions supported by the scientific evidence?
On lines 233 and 234 the authors suggest that riparian buffer zone s are one of the most effective tools for mitigating non-point source pollutants. This is true fo r non-point source pollutants such as nutrients and sediments that might enter riparian areas in groun dwater and runoff, but may not be true for other pollutants such as road salts and organic compounds. I think we need to be careful of promoting riparian areas as a cure for all ills while still clearly indica ting where they are useful. Given the length of the document and its focus on downstream effects the author may not need to address this comment in their final edits.Joel W. Snodgrass, Ph.D.

A-91 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE b) Does the report include the most relevant peer-revie wed literature on these topics, including evidence of connectivity and isolation? If not please i ndicate which references are missing.
To the best of my knowledge in this area the report does incl ude the most relevant literature. However, this is not my area of expertise as I have conducted li ttle work in floodplain systems.

c) Was the reviewed literature cited and summarized cor rectly? If not please indicate where correction or revision is needed.
To the best of my knowledge in this area the report does corr ectly interpret and cite the literature. However, this is not my area of expertise as I have conduc ted little work in floodplain systems.

3. This report concludes that for non-riparian/non-flood plain wetlands that are not connected to the river network through a stream channel (i.e., geographical ly isolated wetlands and wetlands that spill into losing streams), connectivity and isolation vary wit hin a watershed and over time, making it difficult to generalize about their connection s to, or isolation from, downstream waters. The literature we reviewed does not provide sufficient information to evaluate the degree of connectivity (absolute or relative) of these non-riparian particular wetlands.

a) Are these conclusions supported by the scientific evidence?
The authors use the indirect argument that headwater strea ms are widespread and high rates of a number of ecological processes have been measured; therefore, thes e systems must have an impact on downstream rivers. In fact, this is a general approach tha t is well founded (lines 450 through 452). However, in places the authors indicate both pieces of this argument are in place for geographically isolated wetlands—high rates of nutrient removal and exten sive coverage of geographically isolated wetlands—but then only report that the effects of this remov al are not reported for downstream waters (see lines 313 through 328). Although conclusion number 4 below begin s to address this issue, I think the argument could be made more forcefully. In fact, w hat we know about the effects of impervious surface (only mentioned briefly on line 1360) makes a strong argume nt for a large impact of wetland loss in any watershed where wetlands cover a relatively lar ge area—if 25% of a watershed is covered in wetlands and those wetlands are converted to impervious (or l ess pervious) surfaces then there will be large impacts on streams, stream hydrology, geomorphology, eco system function, and biological communities, ultimately affecting downstream rivers (Paul a nd Meyer, 2001; Welsh et al., 2005). The same argument for agricultural systems can be found on lines 1394 through 1400. Given that the depressions that form these wetlands are areas of low or n o surface runoff, a principle we have put to use in our design and management of stormwater runoff using stormwater management ponds, it is highly likely that loses of geographically isolated wetland s have a disproportionally large influence on downstream waters compared to upland habitat loss. Therefo re, it seems that in many areas (e.g., Atlantic and Gulf Coastal Plains) the indirect argument for connection and influence of geographically isolated (but not hydrologically isolated) wetland to downstre am streams and rivers is stronger than the authors indicate with this conclusion. See my general post m eeting comments for further discussion of this issue.Joel W. Snodgrass, Ph.D.

A-92 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE The authors discuss “isolated wetlands that have no hydrologi cal connection to other water bodies” (lines 351 and 352) in a number of places in the manuscript. I am not aware of a hydrological study of an isolated wetland that has not shown some degree of connec tion to ground waters (either through recharge or discharge and recharge). If such studies exis t it might be a good idea to give an example and indicate the number of studies that have found no connection. Additionally, lines 1206 through 1209 describe geographically isolated wetlands that recharge dee p ground water or that occur in isolated terminal basins where “evapotranspiration is the only form of water loss.” I am not familiar with these systems as I work in areas where extensive shallow groundwa ter connections are common. There is no citation with these descriptions either. It would be nice to describe how many studies fit these descriptions and if they are limited to desert springs and lake systems such as the Great Salt Lake. Figure 3-18 makes it seem like these systems can be small a nd similar to geographically isolated wetlands.
Also related to the above comments, in the case study of Caro lina bays the authors suggest that groundwater and surface water connections of bays to stream s are still debated. However, all of the studies to date have documented groundwater connections and the loss and recolonization of these systems by fishes suggests frequent surface water connections for bays up to 700 m from intermittent streams (see Snodgrass et al., 1996 and summary argument in Sharitz 2003). Given these considerations it appears that for Carolina bays at least, connectivity is the norm and isolation rare.
On lines 3521 through 3522 the authors indicate that they “consider any evidence of connectivity with a stream to be evidence of connectivity with the river and ot her downstream waters.” Later (on lines 4097-4098) the authors indicate wetlands that feed losing stream s cannot be considered channel wetlands. However, in the previous chapter the authors argue t hat losing streams should be considered connected to more permanently flowing downstream waters.

b) Does the report include the most relevant peer-revie wed literature on these topics, including evidence of connectivity and isolation? If not please i ndicate which references are missing.
The issues discussed above concerning the importance of is olation for headwater stream communities also applies to geographically isolated wetlands. As the a uthors clearly review, isolated wetlands are periodically connected by surface waters to downstream areas that may provide sources of colonist that establish populations in wetlands. These populations can ha ve large effects on wetland communities through predation, and trade-offs among the competing demands o f surviving desiccating conditions and predation pressures creates adaptations to narrow ranges o f hydrological and predator community conditions (Wiggins et al., 1980; Wellborn et al., 1996). Theref ore, alteration of the isolation or connection of wetlands to downstream communities has the pot ential to alter biodiversity associated with isolated wetlands. See Snodgrass et al. (2000) for furt her discussion in relationship to wetland regulations.

c) Was the reviewed literature cited and summarized cor rectly? If not please indicate where correction or revision is needed.
The literature that was reviewed appears to be interprete d correctly and cited appropriately.Joel W. Snodgrass, Ph.D.

A-93 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE 4. This report concludes that while the influence of a particular stream or wetland on downstream waters might be small, the aggregate contribution by an entire class of streams or wetlands (e.g., all ephemeral streams in the river network, or a cluster of small wetlands) might be substantial.

a) Is this conclusion supported by the scientific evi dence?
Yes the report clearly supports the idea that some wetland s and streams (if not all) make substantial contributions to the structure and functioning of downstream wat ers.
b) Does the report include the most relevant peer-revie wed literature on this topic? If not please indicate which references are missing.
Yes, if the references mention above are included.

c) Was the reviewed literature cited and summarized cor rectly? If not please indicate where correction or revision is needed.
Yes, again with the consideration of comments included abo ve.

Minor notes and typos: Lines 794-794: should also include connection of floodplain wetlands to each other as a critical function of overbank flow. Many species are found associated only with fl oodplain wetlands and depend on overbank flows to connect floodplain wetlands for dispersal.
Line 826: delete “has”—should be “This water can alter ge omorphology...”
Line 900: replace colon with period.
Line 998: add “is”—should be “...the entire river system is diffi cult.”
Lines 1445-1453: this paragraph describes a study, but does not repor t the findings, leaving the reader wondering about the importance of the study.
Lines 1458-1459: given the sheer number of potholes and other types of geographically isolated wetlands it is unlikely we will ever know conditions at even a moderate frac tion of these systems. Does this mean we cannot draw any conclusions regarding these systems?
Line 1646: no paragraph needed here
Line 1677: delete “s” from “recharges”—should be “...ephemeral st reams recharge groundwater...”Lines 2066-2067: tighten—for example, “Mulholland et al. (2008) estimated that small streams ...”

Lines 3933-3934: revise to read “... when connections between wetlands and surface waters are present.”
Lines 2347-2348: flow—“... Los Alamos Canyon resulting from untreated discharge, and less than 2% ...”

Line 7040: no volume number for this reference.Joel W. Snodgrass, Ph.D.

A-94 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE Literature Cited
Butler, D. R., and G. P. Malanson. 2005. The geomorphic inf luences of beaver dams and failures of beaver dams. Geomorphology 71:48-60.
Brooks, R. T., and E. A. Colburn. 2011. Extent and channel morphol ogy of unmapped headwater stream segments of the Quabbin Watershed, Massachusetts. Journal of the American Water Resources Association 47:158-168. DOI: 10.1111/j.1752-1688.2010.00499.x
Dieterich, M., and N. H. Anderson. 2000. The invertebrate faun a of summer-dry streams in Western Oregon. Archives fur Hydrobiologie 147:273-295.
Fend, S.V., and R.O. Brinkhurst. 2000. New species of Rhynchelm is (Clitellata, Lumbriculidae), with observations on the Nearctic species. Hydrobiologia 428:1-59.
Fend, S.V., and D.L. Gustafson. 2001. A new lumbriculid genus and species from North America (Clitellata, Lumbriculidae). Hydrobiologia 463:13-22.
Naiman, R.J., C. A. Johnston, and J. C. Kelley. 1988. Al teration of North American streams by beaver. BioScience 38:753-762.
Naiman, R. J., G. Pinay, C. A. Johnston, and J. Past or. 1994. Beaver influences on the long-term biogeochemical characteristics of a Boreal Forest draina ge network. Ecology 75:905-921. Paller, M. H. 1994. Relationships between fish assemblage st ructure and stream order in South Carolina Coastal Plain streams. Transactions of the American F isheries Society 123:150-161.
Paul, M. J., and J. L. Meyer. 2001. Streams in the urban la ndscape. Annual Review of Ecology and Systematics 32:333–365.
Peterman, W., J. Crawford & R. Semlitsch. 2008. Productiv ity and significance of headwater streams: population structure and biomass of the black-bellied salama nder (Desmognathus quadramaculatus). Freshwater Biology 53:347–357.
Pollock, M. M., M. Heim, D. Werner. 2003. Hydrologic and geomorphic effects of beaver dams and their influence on fishes. American Fisheries Society Symposiu m 37:213-233. Roy, V., M. Amyot, and R. Carignan. 2009. Beaver ponds incre ase methylmercury concentrations in Canadian Shield streams along vegetation and pond-age gradi ents. Environmental Science & Technology 43:5605–5611.
Snodgrass, J. W. 1997. Temporal and spatial dynamics of be aver-created patches as influenced by management practices in a southeastern landscape. Journal of Applied Ecology 34:1043-1056.
Snodgrass J., Forester D., Lahti M. & Lehman E. 2007. Dusky salamander (Desmognathus fuscus) nest-site selection over multiple spatial scales. Herpetologica, 63:441 –449.
Snodgrass, J. W., M. J. Komoroski, A. L. Bryan Jr., an d J. Burger. 2000. Relationships among isolated wetland size, hydroperiod and amphibian species richness : implications for wetland regulations. Conservation Biology 14:414-419.Joel W. Snodgrass, Ph.D.

A-95 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE Snodgrass, J. W., and G. K. Meffe. 1998. Influence of beave rs on stream fish assemblages: effects of pond age and watershed position. Ecology 79:928–942. Stevens, C. E., C. A. Paszkowski, G. Scrimgeour. 2006. Older i s better: beaver ponds on boreal streams as breeding habitat for the wood frog. Journal of Wildlife Man agement 70:1360–1371.
Walsh, C. J., A. H. Roy, J. W. Feminella, P. D. Cott ingham, P. M. Groffman, & R. P. Morgan. 2005. The urban stream syndrome: current knowledge and the search for a c ure. Journal of the North American Benthological Society 24:706-723.
Wellborn, G. A., D. K. Skelly, and E. E. Werner. 1996. Mechanisms creating community structure across a freshwater habitat gradient. Annual Review of Ecology and S ystematics 27:337-363.
Wiggins, G. B., R. J. MacKay, and I. M. Smith. 1980. Evoluti onary and ecological strategies of animals in annual temporary pools. Archives fur Hydrobiologia 58(supplement) :97-206.

Post-Meeting Comments As a general comment concerning the conceptual model introduced a t the beginning of the document I think it would be a good idea to introduce both dimensions of ti me and space and link them to the ideas of sources, sinks, refuges, lags, and transformation. What we really have is a hill-slope to downstream river gradient where things that at the very top of a watershed (i.e., streams and wetlands) are more distantly removed from larger rivers downstream. In a sense the isola tion of these headwaters and wetlands in the top of the watershed makes them sites of significant lag (e.g ., water storage) and therefore potential transformation (could also be thought of as reduced spiral ing length if the concept is applied to the entire gradient). Because streams and wetlands are most spati ally removed from larger rivers, their individual effects will be relatively smaller and take longer periods of time to measure. However, the cumulative effect of their loss will be greater than closer streams and wetlands over the long-term. These connections between scales of time, space and the impacts of disturbance are discussed extensively in Delcourt et al. (1983). The development of the conceptual model in this way would allow the l ogical extension of the review to include the arguments presented earlier on the impacts of impervi ous surfaces and agricultural land conversion discussed in my original comments.
On a related note to the development of the conceptual view, s ome changes to table 3-1 would help with clarity. I do like the idea of not having a specific sequenc e of wetland, stream, and river. Yes, larger rivers are usually downstream (but may not be when rivers enter dese rts), but wetlands and streams can occur in a sequence or be close to or relatively far removed from la rge rivers. The examples I would cite here are adventitious streams verse true headwater streams (See Os born and Wiley’s work that you currently cite) and channel wetlands along stream corridors (see Webster e t al., 1996; Kratz et al., 1997; Magnuson et al., 1998; Baines et al., 2000; Riera et al., 2000; Webster et al., 2000 for an example in Wisconsin lakes, which are formed in the same way pothole wetlands are formed) . Soranno et al. (1999) also argues for the connection between wetlands, lakes and streams based on wat er chemistry in these same systems. Despite the intentions of the authors’ use of arrow in table 3-1, the arrows should be removed as they give the impression of an upstream/downstream gradient.Joel W. Snodgrass, Ph.D.

A-96 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE As far as the question concerning terminology for “geographic ally isolated wetlands,” it might be best to focus the terminology on the hill slope-downstream river gradi ent. Channel origin wetlands should really be considered floodplain wetlands, as they are directly adjac ent to a stream. The definition of floodplain wetlands would be those wetlands that occur on the floodplai n of river systems (as defined by hydrology) or located within or directly adjacent to stream channels or lakes. By the way, the lake situation is completely ignored in the document. This group of wetlands would then include beaver ponds, channel origin wetlands, and wetlands and small lakes situated along stream channel (not necessarily acting as an origin of the channel). This would be more inclusive. Then you could have hill-slope wetlands replace the non-floodplain channel origin group. Hill-slope wetlands are wetlands that are not located directly adjacent to streams and lakes or on the floodplains of rivers. This would still be a very diverse group of wetlands with a range of connectivity, but would be much less confusing. I think the int ent is to convey the idea that for some hillslope wetlands we do know something about connectivity, but for ot her we do not.
Finally, Catherine Pringle’s work in tropical streams pr ovides another example of the influence of connectivity of low-land rivers to headwater streams on communi ty production and structure, which should transfer into altered downstream influences (although I don ’t think here work measured this specifically). References are Pringle et al., 1993, 1999; Pringle and Blake, 1994; Pringle, 1996; Crowl et al., 2001; March et al., 2001, 2002.

Literature Cited
Baines SB, Webster KE, Kratz TK, Carpenter S, Magnuson JJ . 2000. Synchronous behavior of temperature, calcium and chlorophyll in lakes of northern Wisconsin.. Ecol ogy. 81:815-25.
Crowl TA, McDowell WH, Covich AP, Johnson SL. 2001. Freshw ater shrimp effects on detrital processing and nutrients in a tropical head-water stream. Ecology 82: 775–783.
Delcourt, H. R., P. A. Delcourt, and T. Webb. 1983. Dynamic plant ecology: the spectrum of vegetation change in space and time. Quarterly Science Review 1:153-175.
Kratz TK, Webster KE, Bowser CJ, Magnuson JJ, Benson BJ. 1997. The influence of landscape position on lakes in northern Wisconsin. Freshwater Biology. 37:209-17.
March JG, Benstead JP, Pringle CM, Ruebel MW. 2001. Linking shrimp assemblages with rates of detrital processing along an elevational gradient in a tropical st ream. Canadian Journal of Fisheries and Aquatic Sciences 58: 470–478.
March JG, Pringle CM, Townsend MJ, Wilson AI. 2002. Effect s of freshwater shrimp assemblages on benthic communities along an altitudinal gradient of a t ropical island stream. Freshwater Biology 47: 377–390.
Pringle CM. 1996. Atyid shrimps (Decapoda: Atyidae) influen ce the spatial heterogeneity of algal communities over different scales in tropical montane strea ms, Puerto Rico. Freshwater Biology 35: 125–140.Joel W. Snodgrass, Ph.D.

A-97 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE Pringle CM, Blake GA, Covich AP, Buzby KM, Finley A. 1993. Eff ects of omnivorous shrimp in a montane tropical stream: sediment removal, disturbance of sessile invertebrates and enhancement of understory algal biomass. Oecologia 93: 1–11.
Pringle CM, Blake GA. 1994. Quantitative effects of atyid s hrimp (Decapoda: Atyidae) on the depositional environment in a tropical stream: use of electricity for e xperimental exclusion. Canadian Journal of Fisheries and Aquatic Sciences 51: 1443–1450.
Pringle CM, Hemphill N, McDowell WH, Bednarek A, March JG. 1999. Linking species and ecosystems: different biotic assemblages cause interstream difference s in organic matter. Ecology 80: 1860–1872. Riera JL, Magnuson JJ, Kratz TK, Webster KE. 2000. A geomorphi c template for the analysis of lake districts applied to Northern Highland Lake District, Wis consin, U.S.A.. Freshwater Biology. 43:301- 18.
Soranno PA, Webster KE, Riera JL, Kratz TK, Baron JS, Bukaveckas PA, Kling GW, White DS, Caine N, Lathrop RC et al.. 1999. Spatial variation among lakes wi thin landscapes: ecological organization along lake chains.. Ecosystems. 2:395-410.
Webster KE, Soranno PA, Baines SB, Kratz TK, Bowser CJ, Dillon PJ, Campbell P, Fee EJ, Hecky RE. 2000. Structuring features of lake districts: landscape contro ls on lake chemical responses to drought.. Freshwater Biology. 43:499-515.
Webster, K.E., T.K. Kratz, C.J. Bowser, J.J. Magnuson, and W.J. Rose. 1996. The influence of landscape position on lake chemical responses to drought in northern Wi sconsin, USA. Limnol. Oceanogr. 41:977-984.A-99 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE



### Arnold van der Valk, Ph.D.

Professor Department of Ecology, Evolution & Organismal Biology

Iowa State University Ames, IA

Arnold G. van der Valk is a professor in the Department o f Ecology, Evolution and Organismal Biology at Iowa State University. He has a B.Sc. in Biology from the U niversity of Windsor, Canada; an M.Sc. in Botany (Plant Ecology) from the University of Alberta, Cana da; and a Ph.D. in Botany (Plant Ecology) from North Carolina State University. Wetland vegetation dynami cs, landscape differentiation within wetlands, and wetland restoration are his primary research intere sts. He has been an author or editor of 7 books on various aspects of wetland ecology, including three on northe rn prairie wetlands. He has also been an author or co-author over one hundred, peer-reviewed research papers on wetlands that were published in a variety of journals (Applied Ecology, Canadian Journal of Botany, Ecology, Journal of Ecology, Plant Ecology, Restoration Ecology, Wetlands, Wetland Ecology and management , etc.). He is a fellow of the Society of Wetland Scientists and winner of its Merit Award.Arnold van der Valk, Ph.D.

A-101 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE 

### Peer Review Meeting of EPA’s Draft Report: Connectivity of Streams and Wetlands to Downstream Waters – A Review and Synthesis of the Scientif ic Evidence
Comments submitted by Dr. Arnold van der Valk

This report does a very good job of reviewing the massive lite rature on the linkages between streams and wetlands and rivers. It does a particularly good job at dem onstrating the linkages between streams and rivers and between wetlands on floodplains and rivers. It does l ess well in dealing with “isolated” wetlands. In large part this is due to lumping all kinds of non-riparian/non-flood plain wetlands into one category, Non-Riparian and Channel Origin Wetlands.

1. This report concludes that all streams, regardless of flow duration or size, are physically, chemically, and biologically connected to rivers; and these connections, individually or cumulatively, exert a strong influence on the character an d functioning of downstream waters.

a) Are these conclusions supported by the scientific evidence?
Yes. Although I am not a hydrologist or stream ecologist, this is clearly demonstrated in the literature cited.

b) Does the report include the most relevant peer-revie wed literature on these topics, including evidence of connectivity and isolation? If not please indicate which references ar e missing.
Again, I am not a hydrologist, this review, however, cites a large number of relevant references to document the connectivity of streams to rivers. I doubt that any additional references would in any way alter the conclusions drawn.

c) Was the reviewed literature cited and summarized cor rectly? If not please indicate where correction or revision is needed.
I am not an expert on hydrology, but I did not find any obvious pr oblems with literature citations or with the interpretations of the literature.

2. This report concludes that open water and wetlands in riparian areas and floodplains of streams and rivers are physically, chemically, and biologically connect ed with the river network, and that their functions exert a strong influence on the char acter and functioning of downstream waters.

a) Are these conclusions supported by the scientific evidence?
Yes. The multiple connections (surface water, groundwater, biological) between rivers and floodplain wetlands were well documented.Arnold van der Valk, Ph.D.

A-102 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE b) Does the report include the most relevant peer-revie wed literature on these topics, including evidence of connectivity and isolation? If not please indicate which references ar e missing.
The relevant literature on floodplains is huge and unequivoc al about the connectivity of rivers and their floodplains. Although this review does not cite some relevant literature on floodplain development (e.g., J. S. Bridge. 2003. Rivers and Floodplains: Forms, Processes , and Sedimentary Record. Blackwell), it cites the most relevant reviews on connectivity between ri vers and floodplains like Amoros and Bornette (2002). Again, I doubt that the conclusions drawn from the lit erature reviewed would be affected in any way because some relevant references were not included.
Some relevant papers from outside NA that are missing inclu de:

Boschilia, S.M., E.F. Oliveira, and S.M. Thomaz. 2008. Do aquatic macrophytes co-occur randomly? An analysis of null models in a tropical floodplain. Oecologi a 156: 203-214.
Henry, C.P., C. Amoros, and N. Roset. 2002. Restorationecology of riverine wetlands: a 5-year postoperation survey on the Rhone River, France. Ecological Engineer ing 18: 543-554. Paillex, A., S. Doledec, E. Castella, and S. Merigoux. 2009 . Large river floodplain restoration: predicting species richness and trait responses to the restoration o f hydrological connectivity. Journal of Applied Ecology 46: 250-258.
Vervuren, P.J.A., C.W.P.M Blom and H. de Kroon. 2003. Extrem e flooding events on the Rhine and the survival and distribution of riparian plant species. Journal of Ecology 91: 135-146.

c) Was the reviewed literature cited and summarized cor rectly? If not please indicate where correction or revision is needed.
I am not an expert on riverine hydrology, but I did not find any obvious problems with literature citations or with the interpretations of the literature.

3. This report concludes that for non-riparian/non-flo odplain wetlands that are not connected to the river network through a stream channel (i.e., geographical ly isolated wetlands and wetlands that spill into losing streams), connectivity and isolation vary wit hin a watershed and over time, making it difficult to generalize about their connections to, or isolation from, downstream waters. The literature we reviewed does not provide sufficient infor mation to evaluate the degree of connectivity (absolute or relative) of these non-riparian particular w etlands.

a) Are these conclusions supported by the scientific evidence?
Yes. This category of wetlands, however, contains a mix o f wetland types that is so broad and heterogeneous that no definitive conclusions about their hydrologic al connectivity to rivers could ever be drawn for the entire category. There are situations whe re a case for hydrologic connectivity of wetlands in this class to rivers can be made using soils data, e.g., prairie potholes in Iowa. Although definitive data are missing in most cases, it can be inferred that these t ypes of wetlands are connected biologically to rivers and vice versa in many, if not all, cases.Arnold van der Valk, Ph.D.

A-103 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE b) Does the report include the most relevant peer-revie wed literature on these topics, including evidence of connectivity and isolation? If not please indicate which references ar e missing.
Yes. It does a good job of reviewing the published literature . However, it is somewhat ambivalent about the interpretation of some of the literature on “clusters” of wetlands. Although wetlands within a cluster evidently are linked, presumably by groundwater flows, they a re considered only linked if there is a surface water connection from one wetland in the cluster to a river. The potential for groundwater connections between isolated wetlands and rivers is never exa mined. That wetlands like prairie potholes are connected by groundwater flows is well documented. Tha t similar groundwater flows can also connect them to rivers is at least highly probable for some pra irie potholes in less hummocky terrain.

c) Was the reviewed literature cited and summarized cor rectly? If not please indicate where correction or revision is needed.
Yes. However, the use of soil maps, however, to demonstrate e phemeral surface water linkages between isolated wetlands like prairie potholes and streams is not f ully explored. See above. Likewise the possible connection of isolated wetlands to rivers by groundwater flow is largely ignored.

4. This report concludes that while the influence of a particular stream or wetland on downstream waters might be small, the aggregate contribution by an entire class of streams or wetlands (e.g., all ephemeral streams in the river network, or a cluster of small wetlands) might be substantial.

a) Is this conclusion supported by the scientific evi dence?
For streams, this conclusion is self-evident and is supporte d by the literature. For isolated wetland complexes, there are only a few relevant studies. Conseq uently, although it may be true, it is more of a conjecture than a fact. What exactly constitutes “a cluste r of small wetlands”? How do you draw the boundaries around a cluster? See above.

b) Does the report include the most relevant peer-revie wed literature on this topic? If not please indicate which references are missing.

Yes, the most relevant literature has been reviewed in the report. However, the relevant literature on wetland soils that demonstrates how connected some putatively isolated wetlands like prairie potholes really are is not adequately explored. See Miller et al . (2012) in Wetland Ecology and Management.

c) Was the reviewed literature cited and summarized cor rectly? If not please indicate where correction or revision is needed.
Yes. The problem is not with the interpretation of the lit erature but with creating an artificial category of wetlands that contains so many different kinds of wetlands that no general conclusion could ever be drawn for the entire category.Arnold van der Valk, Ph.D.

A-104 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE Some Additional Comments
The main purpose of this report is to demonstrate the connect ivity between streams and wetlands and navigable rivers. There are a large number of papers tha t have been published in the landscape ecology literature on connectivity and how to measure it. This liter ature is largely ignored in this report. A review of what is meant by connectivity and the various relevant wa ys in which streams and wetlands may be linked to rivers is needed. In fact, the whole report might have been more usefully organized around various kinds of linkages with chapters on surface water flows, groundwater flows, wind, and various animal vectors and their relative influences on navigable rivers. One of the major dil emmas facing the reviewers was that hydrological linkages are better studied and thus are much easier are to demonstrate than biological linkages. Not surprisingly the report emphasizes hydrological connectivity. Bi ological linkages are often sporadic and highly species specific and are thus harder to document. Most of the focus on biological connectivity in the report is on fish movements into and out of wetlands on floodpla ins. Because isolated wetlands are linked to rivers primarily by biological linkages, I believe that this report seriously underestimates the connectivity between isolated wetlands and rivers. The literature on waterbird (ducks, geese, cranes, etc.) migratory and local movements, which is largely ignored in the report, is full of accounts of birds moving from wetlands to rivers and vice versa, e.g., Canvasbacks in the Mississi ppi River flyway. In the case study on prairie potholes, however, there is a good synthesis of the evidence for both hydrological and biological connectivity of potholes to rivers. In short, I think that a stronger case can be made that some of the wetlands in the isolated wetland category are connected to rivers.
I found the Non-Riparian and Channel Origin (NRCW) class of wetlands created in this report unnecessary and confusing. In fact, the term NRCW is never used in the Executive Summary. For the most part, this term is used a catchall for non-riparian/non-floodplain wetlands. The common denominator that supposedly justifies putting prairie potholes and other isolated wetlan ds in the same class as wetlands that are the headwaters for streams (channel origin wetlands) is unidirec tional surface flow (P. 42, ll. 813-815). Although some isolated wetlands like prairie potholes during high wat er events do have temporary surface connections to each other and even to nearby streams, many do not as n oted. Many headwater wetlands, however, can have water backing up into them from streams during flooding e vents. It would be simpler to eliminate the use of the NRCW class from the report. The problem with l umping these two types of wetlands together is illustrated on P. 206 ll. 4292-4294: “NRCWs, however, are generally farther from stream channels than riparian/floodplain wetlands, which make hydrologic connectivity much less frequent, if present at all.” This statement is by definition untrue for channel origin wetlan ds.

Instead of the artificial NRCW class of wetlands, it would be more useful to follow the Cowardin et al. (1979) classification of wetlands which distinguishes five basic types (systems) of wetlands, only three of which are relevant in this context, (riverine, palustrine, and lacustr ine). As defined by Cowardin et al. (1979), “The term SYSTEM refers here to a complex of wetlands and deepwater h abitats that share the influence of similar hydrologic, geomorphologic, chemical, or biological factors.” Co wardin et al., recognize that intermittent streams are connected to perennial reaches of streams. The y are treated as part of the riverine system. Lacustrine wetlands are found along the peripheries of lakes , and there is absolutely no doubt that they are connected to navigable water. What is being examined in this report is the connectivity between rivers and various kinds of palustrine wetlands. Palustrine wetlands are bounded by uplands. There are many kinds of palustrine wetlands, and they are found “shoreward of lakes, river channels, or estuaries; on river floodplains;Arnold van der Valk, Ph.D.

A-105 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE in isolated catchments; or on slopes.” In other words , this report should focus on the connectivity of different kinds of palustrine wetlands. This ranges from those clearl y linked to rivers like palustrine wetlands on floodplains to those with much weaker linkages like palustrine wetlands in isolated catchments like many inter-mountain wetlands. In the case of palustrine wetla nds that generally have no surface water connections to rivers, each major type should be treated separately (prairie potholes, California vernal pools, Carolina bays, Texas playas, etc.)
The Cowardin et al., classification systems is used by t he National Wetland Inventory. Discussing the connectivity of palustrine wetlands to rivers would make it i mmediately obvious to readers familiar with wetlands what this report is trying to do, and it would link the report more directly to the existing wetland literature.
Five functions of streams and wetlands are recognized (P. 5, ll. 106-113). I would suggest renaming the last one, Lag, Desynchronization. A lag is an effect, not a fu nction.
What is the relative importance of hydrological vs. biologic al connectivity? It is possible for some types of wetlands to have no surface water connection to streams. Gi ven that all wetlands have hydric plants and a host of aquatic animals (invertebrates, birds, mammals, microo rganisms, etc.), even hydrologically isolated wetlands are never isolated biologically. What species should count in establishing biological connectivity? In the report, all microorganisms (algae, bacteria, fungi, protozoans, etc.) are essentially ignored. Although the report does a good job in demonstrating the ubiquity of biological connectivity, it is unclear how important this type of connectivity is when compared to hydrological connect ivity and what minimum criterion or threshold is required to demonstrate biological connectivity. Doe s demonstrating the one-time movement or dispersal of one species from a river or a stream to a h ydrologically isolated wetland (or vice versa) mean that the “isolated” wetland is not really isolated? If just e stablishing some kind of biological linkage between a wetland and a river establishes connectivity, then there is no such thing as an isolated wetland.
When looking for linkages between “isolated” wetlands and ri vers, a landscape approach is needed. One possible way to examine these linkages would be to use an H GM approach to estimate water, sediment, nutrient, etc. storage by the wetlands in a watershed and thus not entering the rivers. Potential linkages of various animal groups and wind could also be explored using t his general approach. The more linkages that can be demonstrated the greater the influence of isolated w etlands in a watershed (or other comparable landscape unit) on the rivers in it.
In summary, the authors of the report focus primarily on s urface water flows as the major link between rivers and streams and wetlands. This primarily unidirectional f low of water into rivers is easy to demonstrate and its importance can be quantified. The more complex and often sporadic and bidirectional linkages caused by wind and movement of organisms are noted, but their influ ence on navigable waters has rarely been documented. Whether such movements are essential for the pers istence of some organisms in rivers is unknown. That some organisms (some waterfowl, some mammals, some amphibians) use both rivers and isolated wetlands during their life cycles is known. As a c onsequence, in any landscape all bodies of water are interconnected and influence each other, but these interact ions are often sporadic and asymmetrical.A-107 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE



### Mark S. Wipfli, Ph.D. Professor U.S. Geological Survey Cooperative Fish & Wildlife Researc h Unit

Institute of Arctic Biology University of Alaska Fairbanks, AK

Education -- Ph.D., 1992, Michigan State University, Aquatic Ecology & Environmental Toxicology; M.Sc., 1987, University of Wisconsin Madison, Entomology; B.S c., 1984, University of Wisconsin Madison, Natural Science

Dr. Wipfli’s research interests include understanding:

• Trophic linkages between headwaters and downstream habitats

• Trophic processes that govern freshwater-riparian productivi ty

• Spatial subsidies in freshwater food webs

• Linkages between freshwater-marine and freshwater-terrest rial ecosystems

• Salmonid foraging ecology and trophic interactions

• Invasive species impacts in freshwater/riparian ecosyste ms

• Climate change effects on freshwater food webs

• Restoration and management of freshwater and riparian ec osystems

He has published in Canadian Journal of Fisheries and Aquat ic Sciences, Transactions of the American Fisheries Society, North American Benthological Society, Freshwater Biology, Hydrobiologia, Oecologia, BioScience, Fisheries, and others

Selected publications relevant to the workshop: Wipfli, M.S., and C.V. Baxter. 2010. Linking ecosystems, f ood webs, and fish production: Subsidies in salmonid watersheds. Fisheries 35(8): 373-387.
Binckley, C., M.S. Wipfli, R.B. Medhurst, K. Polivka, P. Hessburg, B. Salter, and J.Y. Kill. 2010. Ecoregion and land-use influence invertebrate and detritus tr ansport from headwater streams. Freshwater Biology 55: 1205-1218.
Medhurst, R.B., M.S. Wipfli, K. Polivka, C. Binckley, P. Hessburg, and B. Salter. 2010. Headwater streams and forest management: Does ecoregional context influence loggi ng effects on benthic communities? Hydrobiologia 641: 71-83.
Wipfli, M.S., J.S. Richardson, and R.J. Naiman. 2007. Ecol ogical linkages between headwaters and downstream ecosystems: transport of organic matter, inve rtebrates, and wood down headwater channels. Journal of the American Water Resources Assoc iation 43: 72-85.
Gomi, T., A.C. Johnson, R.L. Deal, P.E. Hennon, E.H. Orl ikowska, and M.S. Wipfli. 2006. Factors affecting distribution of wood, detritus, and sediment in headwa ter streams draining managed younggrowth red alder-conifer forests in Southeast Alaska. Can adian Journal of Forest Research 36: 725- 737.A-108 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE Hernandez, O., R.W. Merritt, and M.S. Wipfli. 2005. Benthic invertebrate community structure in headwater streams is influenced by forest succession af ter clearcut logging in southeastern Alaska. Hydrobiologia. 533: 45-59.
Wipfli, M.S. and J. Musslewhite. 2004. Density of red alder ( Alnus rubra ) in headwaters influences invertebrate and organic matter subsidies to downstream fis h habitats in Alaska. Hydrobiologia. 520: 153-163.
Piccolo, J.J., and M.S. Wipfli. 2002. Does red alder ( Alnus rubra ) along headwater streams increase the export of invertebrates and detritus from headwaters to fish -bearing habitats in southeastern Alaska? Canadian Journal of Fisheries and Aquatic Sciences. 59: 503- 513.
Wipfli, M.S., and D.P. Gregovich. 2002. Export of invertebrate s and detritus from fishless headwater streams in southeastern Alaska: implications for downst ream salmonid production. Freshwater Biology. 47: 957-969.Mark S. Wipfli, Ph.D.

A-109 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE 

### Peer Review Meeting of EPA’s Draft Report: Connectivity of Streams and Wetlands to Downstream Waters – A Review and Synthesis of the Scientif ic Evidence

Comments submitted by Dr. Mark S. Wipfli

1. This report concludes that all streams, regardless of f low duration or size, are physically, chemically, and biologically connected to rivers; and these connections, individually or cumulatively, exert a strong influence on the character an d functioning of downstream waters.

a) Are these conclusions supported by the scientific evidence?
Yes, to the best of my knowledge, the conclusions are fully support ed by the evidence in the scientific literature. There is strong evidence in the scientific l iterature that headwaters are physically, biologically, and chemically connected to, and influence, downstream wat ers and associated biota. The evidence reported and cited in this review is presented accurate ly, thoroughly, and clearly.

b) Does the report include the most relevant peer-revie wed literature on these topics, including evidence of connectivity and isolation? If not please indicate which references a re missing.
Yes, to the best of my knowledge, the report includes a broad, relevant literature on the connections between headwaters and downstream freshwater ecosystems. However, I did not see literature discussed and cited that addresses the linkages between headwaters and estuaries and oceans, even though that point is stated in the first paragraph of “Background” section of “Technical Charge to External Peer Reviews” document. Should this be included?
Five additional references from my headwaters work on biologica l linkages that may be helpful are listed below. The latter four deal with management effects on headw ater streams.
Wipfli, M.S., and C.V. Baxter. 2010. Linking ecosystems, f ood webs, and fish production: Subsidies in salmonid watersheds. Fisheries 35(8): 373-387. This paper takes a broader look at watersheds, putting into context the biological connections between headwaters, rive r networks, riparian habitats, and the ocean.
Binckley, C., M.S. Wipfli, R.B. Medhurst, K. Polivka, P. Hessburg, B. Salter, and J.Y. Kill. 2010. Ecoregion and land-use influence invertebrate and detritus tr ansport from headwater streams. Freshwater Biology 55: 1205-1218. This paper shows how past timber harvesting affects invertebrate flow from headwaters to downstream habitats.
Medhurst, R.B., M.S. Wipfli, K. Polivka, C. Binckley, P. Hessburg, and B. Salter. 2010. Headwater streams and forest management: Does ecoregional context in fluence logging effects on benthic communities? Hydrobiologia 641: 71-83. Addresses past timber harvest effects on headwater stream invertebrate communities.Mark S. Wipfli, Ph.D.

A-110 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE Wipfli, M.S. and J. Musslewhite. 2004. Density of red alder ( Alnus rubra ) in headwaters influences invertebrate and organic matter subsidies to downstream fis h habitats in Alaska. Hydrobiologia. 520: 153-163. This paper showed that headwater streams also supply terrestrial invert ebrates to downstream waters, in addition to aquatic invertebrates, and illustrat ed how riparian management affects biological connections between riparian areas, headwater streams, and downstream waters. Piccolo, J.J., and M.S. Wipfli. 2002. Does red alder ( Alnus rubra ) along headwater streams increase the export of invertebrates and detritus from headwaters to fish -bearing habitats in southeastern Alaska? Canadian Journal of Fisheries and Aquatic Scienc es. 59: 503-513. This paper looks at how riparian regrowth following timber harvest in Alaska affects transpor t of aquatic invertebrates to downstream waters.
Another paper from research we conducted on headwater stream s looking at the role of wildfire in affecting linkages between headwater streams and downstrea m waters, via the flow of invertebrates downstream:
Mellon, C.D., M.S. Wipfli, and J.L. Li. 2008. Effects of forest fire on headwater stream macroinvertebrate communities in eastern Washington, USA. F reshwater Biology 53: 2331–2343.

c) Was the reviewed literature cited and summarized cor rectly? If not please indicate where correction or revision is needed.
Yes, the literature in this report was cited and summa rized accurately. The authors provided a very clear and thorough illustration of the demonstrated linkages that connect headwaters to downstream waterways.
A few points that might help:

Line 1494 – “and associated biota” at the end of the sentence?
Lines 1698, 1709, 1844 – Several places in the text (these two as exam ples) could benefit with a relevant citation.

Lines 1793-4 and 1804-6 seem to be in conflict with each other.
Line 2160 – space before 100.
Line 2375 (whole section) – this would be a good place to discuss the role of terrestrial invertebrates that enter headwaters, and in turn get transported downstream f rom headwaters (Wipfli and Musslewhite 2004). Not sure if the authors would like to have this concept in the report, but it also ties in human impacts into the story.Mark S. Wipfli, Ph.D.

A-111 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE 2. This report concludes that open water and wetlands in riparian areas and floodplains of streams and rivers are physically, chemically, and biologically connect ed with the river network, and that their functions exert a strong influence on the char acter and functioning of downstream waters.

a) Are these conclusions supported by the scientific evidence?
Yes, to the best of my knowledge, the conclusions are fully support ed by the evidence in the scientific literature. There is strong evidence in the scientific l iterature that riparian area wetlands and other waters are physically, biologically, and chemically connected to, a nd influence, the river network. The evidence reported and cited in this review is presented accurate ly, thoroughly, and clearly.

b) Does the report include the most relevant peer-revie wed literature on these topics, including evidence of connectivity and isolation? If not please indicate which references a re missing.
Yes, the report appears to include the most relevant liter ature that shows how off-channel freshwater habitats are connected to mainstem channels and riverine ne tworks.

c) Was the reviewed literature cited and summarized cor rectly? If not please indicate where correction or revision is needed.
Yes, the literature in this report was cited and summa rized thoroughly and correctly.

3. This report concludes that for non-riparian/non-flood plain wetlands that are not connected to the river network through a stream channel (i.e., geographical ly isolated wetlands and wetlands that spill into losing streams), connectivity and isolation vary wit hin a watershed and over time, making it difficult to generalize about their connections to, or isolation from, downstream waters. The literature we reviewed does not provide sufficient infor mation to evaluate the degree of connectivity (absolute or relative) of these non-riparian particular w etlands.

a) Are these conclusions supported by the scientific evidence?
Question is outside my area of expertise.

b) Does the report include the most relevant peer-revie wed literature on these topics, including evidence of connectivity and isolation? If not please indicate which references a re missing.
Question is outside my area of expertise.

c) Was the reviewed literature cited and summarized cor rectly? If not please indicate where correction or revision is needed.
Question is outside my area of expertise.Mark S. Wipfli, Ph.D.

A-112 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE 4. This report concludes that while the influence of a particular stream or wetland on downstream waters might be small, the aggregate contribution by an entire class of streams or wetlands (e.g., all ephemeral streams in the river network, or a cluster of small wetlands) might be substantial.

a) Is this conclusion supported by the scientific evi dence?
Absolutely yes. This is a key point about headwaters and downs tream waterways that unfortunately can easily be overlooked, and I was pleased to see this addres sed. Individually, small streams do generally not have large influences by themselves on downstream processe s, but in aggregate they tremendously affect riverine networks at the watershed scale.

b) Does the report include the most relevant peer-revie wed literature on this topic? If not please indicate which references are missing.
Yes, the report includes the relevant scientific literat ure on the cumulative effects of headwaters.

c) Was the reviewed literature cited and summarized cor rectly? If not please indicate where correction or revision is needed.
Yes, to the best of my knowledge the literature on this topic w as cited and summarized thoroughly and correctly.

Marine-derived nutrient effects on stream productivity
Discussed at the review on 30 Jan, 2012 was the topic of mar ine-derived nutrients, and their effects on headwater productivity in places that receive runs of anadrom ous fishes. It was suggested that a discussion of this topic be included in the report, and I agree tha t it should be included. This phenomenon is demonstrated through runs of adult Pacific salmon throughout the west co ast of North America, but occurs along the east coast with Atlantic salmon, as well as runs of shad, lamprey, and other species, and throughout other parts of the world. Spawning adults deliver nutrients and carbon from t he ocean when they return to fresh water to spawn (and die). This subsidy of nutrients and carbon (energy ) from the ocean has been universally shown to increase stream productivity, including in headwater stre ams, at multiple trophic levels (periphyton, aquatic invertebrates, and fishes). The increased production in headwa ters in turn provides more invertebrates that can get flushed downstream from smaller headwater channels to downs tream waters. Thus, the ocean is connected to headwaters via the movement of marine subsidies into waters heds. In turn a portion of this invertebrate production can subsequently get delivered downstream from headwa ters.
Here are some of my papers on this topic. They in turn con tain numerous additional citations on the subject that can be included in the report, if EPA decides this is a topic worth including.
Wipfli, M.S., J.P. Hudson, J.P. Caouette, N.L. Mitchell , J.L. Lessard, R.A. Heintz, and D.T. Chaloner. 2010. Salmon carcasses increase stream productivity more than i norganic fertilizer pellets: A test on multiple trophic levels in streamside experimental channels. Trans actions of the American Fisheries Society 139: 824-839.Mark S. Wipfli, Ph.D.

A-113 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE Heintz, R.A., M.S. Wipfli, and J.P. Hudson. 2010. Identifica tion of marine-derived lipids in juvenile coho salmon and aquatic insects through fatty acid analysis. Transactions of the American Fisheries Society 139: 840-854.
Lang, D.W., G.H. Reeves, D.D. Hall, and M.S. Wipfli. 2006. The influence of fall-spawning coho salmon (Oncorhynchus kisutch) on growth and production of juvenile coho sa lmon rearing in beaver ponds on the Copper River Delta, Alaska. Canadian Journal of Fis heries and Aquatic Sciences 63: 917-930.
Hicks, B.J., M.S. Wipfli, D.W. Lang, and M.E. Lang. 2005. Marine-derived nitrogen and carbon in freshwater-riparian food webs of the Copper River Delta, so uthcentral Alaska. Oecologia 144: 558-569.
Heintz, R.A., B.D. Nelson, J.P. Hudson., M. Larsen, L. Holland, and M.S. Wipfli. 2004. Marine subsidies in freshwater: Effects of salmon carcasses on the lipid c lass and fatty acid composition of juvenile coho salmon. Transactions of the American Fisheries Society. 133: 559-567.
Wipfli, M.S., J.P. Hudson, J.P. Caouette, and D.T. Cha loner. 2003. Marine subsidies in freshwater ecosystems: salmon carcasses increase the growth rates of stream-resident salmonids. Transactions of the American Fisheries Society. 132: 371-381. Wipfli, M.S., J.P. Hudson, and J.P. Caouette. 1998. Influence of salmon carcasses on stream productivity: response of biofilm and benthic macroinvertebrates in southeas tern Alaska, USA. Canadian Journal of Fisheries and Aquatic Sciences. 55: 1503-1511.

Some additional relevant MDN papers include:
Bilby, R. E., B. R. Fransen, P. A. Bisson, and J . K . Walter. 1998. Response of juvenile coho salmon (Oncorhynchus kisutch) and steelhead (Oncorhynchus mykiss) to the addition of salmon carcasses to two streams in southwestern Washington, USA. Canadian Journal of Fisheries and Aquatic Sciences 55:1909-1918.
Bilby, R. E., Fransen, B. R., Walter, J . K., Cederho lm, C. J ., and W. J . Scarlett. 2001. Preliminary evaluation of the use of nitrogen stable isotope ratios to e stablish escapement levels for Pacific salmon. Fisheries 26:6-14.
Claeson, S. M., J. L. Li, J. E. Compton, and P. A. Bis son. 2006. Response of nutrients, biofilm, and benthic insects to salmon carcass addition. Canadian Journal of Fisheries and Aquatic Sciences 63:1230-1241.
Jonsson, B., and N. Jonsson. 2003. Migratory Atlantic salm on as vectors for the transfer of energy and nutrients between freshwater and marine environments. Freshwa ter Biology 48:21-27.
Nislow, K.H., and B.E. Kynard. 2009. The role of anadromo us sea lamprey in nutrient and material transport between marine and freshwater environments. Amer. Fish Soc. Symp. 69:485-494.
Rand, P. S., C. A. S. Hall, W. H. McDowell, N. H. R ingler, and J. G. Kennen. 1992. Factors limiting primary productivity in Lake Ontario tributaries receiving salmon m igrations. Canadian Journal of Fisheries and Aquatic Sciences 49:2377-2385.Mark S. Wipfli, Ph.D.

A-114 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE Terrestrial prey subsidies
Another topic briefly discussed for possible inclusion in the final report was the trophic linkage between headwater streams and their riparian forests, and how this linkage affects the flow of terrestrial invertebrates from headwater streams to downstream habitats. This is an other avenue thorough which headwater streams are connected to downstream waters. Below are a few refe rences for the report that discuss terrestrial invertebrate subsidies to streams, which in turn contain furt her references the authors of the EPA report can decide on their inclusion.
Allan, J. D., M. S. Wipfli, J. P. Caouette, A. Prussia n, and J. Rodgers. 2003. Influence of streamside vegetation on inputs of terrestrial invertebrates to salmonid food webs. Canadian Journal of Fisheries and Aquatic Sciences 60:309-320.
Baxter, C. V., K. D. Fausch, M. Murakami, and P. L. C hapman. 2007. Invading rainbow trout usurp a terrestrial prey subsidy to native char and alter their be havior, growth, and abundance. Oecologia 153:461-470.
Baxter, C. V., K. D. Fausch, and W. C. Saunders. 2005. Tan gled webs: reciprocal flows of invertebrate prey link streams and riparian zones. Freshwater Biology 50(2):201- 220.
Kawaguchi, Y., and S. Nakano. 2001. Contribution of terrestr ial invertebrates to the annual resource budget for salmonids in forest and grassland reaches of a headw ater stream. Freshwater Biology 46:303-316.
Kawaguchi, Y., S. Nakano, and Y. Taniguchi. 2003. Terrest rial invertebrate inputs determine the local abundance of stream fishes in a forested stream. Ecology 84(3) :701-708.
Mason, C. F., and S. M. MacDonald. 1982. The input of terre strial invertebrates from tree canopies to a stream. Freshwater Biology 12:305-311.
Nakano, S., H. Miyasaka, and N. Kuhara. 1999. Terrestria l-aquatic linkages: riparian arthropod inputs alter trophic cascades in a stream food web. Ecology 80(7):2435-2441. Richardson, J.S., Y. Zhang & L.B. Marczak. 2010. Resource subsidies across the land-freshwater interface and responses in recipient communities. River Research and Applications 26:55-66.
Saunders, W. C., and K. D. Fausch. 2007. Improved grazing man agement increases terrestrial invertebrate inputs that feed trout in Wyoming rangeland streams. Trans actions of the American Fisheries Society 136:1216-1230.A-115 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE



### William R. Wise, Ph.D. Associate Professor Department of Environmental Engineering Sciences

University of Florida Gainesville, FL

Dr. Wise’s pre-meeting comments are included in this rep ort. Dr. Wise was unable to participate in the meeting and therefore was not able to prepare or submit pos t-meeting comments.William R. Wise, Ph.D.

A-117 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE 

### Peer Review Meeting of EPA’s Draft Report: Connectivity of Streams and Wetlands to Downstream Waters – A Review and Synthesis of the Scientif ic Evidence

Pre-Meeting Comments submitted by Dr. William R. Wise

TECHNICAL CHARGE QUESTIONS:



### 1. This report concludes that all streams, regardless of flow duration or size, are physically, chemically, and biologically connected to rivers; and these con nections, individually or cumulatively, exert a strong influence on the character and f unctioning of downstream waters.

a) Are these conclusions supported by the scientific evid ence?
Yes. The physical setting governs the types of material tha t can be transported to the downstream waters. This includes everything from the scale of chemical s and microorganisms to large woody debris, which provides important structure for a variety of aquati c species. Therefore, there is no question that all streams are physically, chemically, and biologically c onnected to the downstream waters, which might be rivers, estuaries, bays, springs, or aquifers. E phemeral flow patterns should in no way be discriminated against because these often occur in region s where flashy events are capable of conveying quite a lot of matter to the receiving waters in a sho rt period of time. Often, due to the different regime of the receiving water body (such as the velocity being great ly reduced), this matter will persist and affect the physical, chemical, and biological character of the receiving body.

b) Does the report include the most relevant peer-reviewed literature on these topics, including evidence of connectivity and isolation? If not please indicate which references a re missing.
All hydrology is local, so this is indeed a difficult quest ion. The fact that the term karst does not appear in the glossary is of major concern to this reviewer. Ka rst systems deserve explicit mention when discussing the connection of water bodies because they often provide “out of sight-out of mind” conduits between seemingly unconnected waters and yet are dir ect exchange mechanisms for waters and their physical (mostly temperature), chemical, and biologic al properties. One reason that this issue deserves special consideration is that karst features usual ly suffer from an inability to attenuate water quality issues from one water body to another, as they do not filter the water as many other hydrologic connections can.
One example of this is the Santa Fe River in North Centra l Florida. It sinks into the ground and reemerges over three miles later. This reviewer has appli ed a common surface water routing model, the Muskingum method, to the underground portion and found that it applies very well. However, the water is underground; so is it a river? While this legal consider ation exceeds the technical charge, it is worth noting that there remain important collaborative efforts to knit together technical and legal interpretations of the “colors of water.”William R. Wise, Ph.D.

A-118 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE Karst systems are not unique to Florida but are prevalen t in many states, such as Texas, Missouri, and Kentucky, to name a few.

c) Was the reviewed literature cited and summarized correc tly? If not please indicate where correction or revision is needed.

The cited literature with which I had direct familia rity was well represented. Spot checking a few others for personal interest verified the same.

2. This report concludes that open water and wetlands in riparian areas and floodplains of streams and rivers are physically, chemically, and biologically connect ed with the river network, and that their functions exert a strong influence on the char acter and functioning of downstream waters.

a) Are these conclusions supported by the scientific evidence?
Yes. Open water and wetlands in riparian corridors provide important refugia for many species. They also, of course, provide conveyance of flow for extreme even ts. Their physical properties, such as vegetative nature and density are extremely important in gove rning the speed in which floods move through a system.
A class of streams known as deranged, where channels flow i nto wetlands and then back into channels is not specifically mentioned. In these systems, it can be difficult to know how to characterize the wetlands, even though there is no doubt of their connectivity to the system. This scenario should be mentioned although the impacts from the findings would not really change.

b) Does the report include the most relevant peer-reviewed literature on these topics, including evidence of connectivity and isolation? If not please indicate which references a re missing.
Again, all hydrology is local, so this is a difficult que stion. The cited literature does effectively address the issue, however.

c) Was the reviewed literature cited and summarized correc tly? If not please indicate where correction or revision is needed.

The cited literature with which I had direct familia rity was well represented. Spot checking a few others for personal interest verified the same.William R. Wise, Ph.D.

A-119 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE 3. This report concludes that for non-riparian/non-flood plain wetlands that are not connected to the river network through a stream channel (i.e., geographical ly isolated wetlands and wetlands that spill into losing streams), connectivity and isolation vary wit hin a watershed and over time, making it difficult to generalize about their connection s to, or isolation from, downstream waters. The literature we reviewed does not provide sufficient information to evaluate the degree of connectivity (absolute or relative) of these non-riparian particular wetlands.

a) Are these conclusions supported by the scientific evidence?
These conclusions are both supported by the scientific lite rature and the extensive experience of this reviewer, who has worked in both what would be termed c onnected and isolated (hydrologically, not just geographically) wetlands.

b) Does the report include the most relevant peer-reviewed literature on these topics, including evidence of connectivity and isolation? If not please indicate which references a re missing.
Again, all hydrology is local, so this is a difficult que stion. The cited literature does effectively address the issue, however.

c) Was the reviewed literature cited and summarized correc tly? If not please indicate where correction or revision is needed.

The cited literature with which I had direct familia rity was well represented. Spot checking a few others for personal interest verified the same.

4. This report concludes that while the influence of a particular stream or wetland on downstream waters might be small, the aggregate contribution by an entire class of streams or wetlands (e.g., all ephemeral streams in the river network, or a cluster of small wetlands) might be substantial.

a) Is this conclusion supported by the scientific evi dence?
Yes. This is absolutely true. At any given point along a wate rway, the watershed is defined as the locus of all points that drain to it. That one stream might seem minor is no reason to treat it differently than a larger stream. Smaller streams dominate geographically and need to be respected in the aggregate, as this conclusion states.

b) Does the report include the most relevant peer-reviewed literature on this topic? If not please indicate which references are missing.
Again, all hydrology is local, so this is a difficult que stion. The cited literature does effectively address the issue, however.

c) Was the reviewed literature cited and summarized correc tly? If not please indicate where correction or revision is needed.

The cited literature with which I had direct familia rity was well represented. Spot checking a few others for personal interest verified the same.B-1 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE



## Appendix B: Meeting AgendaB-3 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE United States Environmental Protection Agency National Center for Environmental Assessment 

# Peer Review Meeting for EPA’s Draft Report: Connect ivity of Streams and Wetlands to Downstream Waters - A Review and Synthesis of the Scientific Evidence

Washington, DC Monday, January 30, 2012 

# Agenda

8:00 AM Meeting Check in

8:30 AM Welcome, Meeting Ground Rules & Logistics

.......................................... **Kate Schalk, ERG (Contractor)**

8:45 AM EPA Remarks

.................................................. ............................................... **Laurie Alexander, EPA/ORD**

REVIEWER INTRODUCTION AND DISCUSSIONS
9:00 AM Discussion of Document Structure and Orga nization ......................... **Walter Dodds (Chair) & Reviewers**

9:30 AM BREAK

9:45 AM Charge Question 1

.................................................. ............................ Walter Dodds ( **Chair) & Reviewers**

This report concludes that all streams, regardless of flow duration or size, are physically, chemically, and biologically connected to rivers; a nd these connections, individually or cumulatively, exert a strong influence on the chara cter and functioning of downstream waters. a) Are these conclusions supported by the scientific e vidence? b) Does the report include the most relevant peer-revi ewed literature on these topics, including evidence of connectivity **and** isolation? If not please indicate which references are missing. c) Was the reviewed literature cited and summarized co rrectly? If not please indicate where correction or revision is needed.

11:15 AM Charge Question 2

.................................................. ............................ Walter Dodds ( **Chair) & Reviewers** This report concludes that open water and wetlands in riparian areas and floodplains of streams and rivers are physically, chemically, and biologic ally connected with the river network, and that their functions exert a strong influence on the cha racter and functioning of downstream waters. a) Are these conclusions supported by the scientific e vidence? b) Does the report include the most relevant peer-revi ewed literature on these topics, including evidence of connectivity **and** isolation? If not please indicate which references are missing. c) Was the reviewed literature cited and summarized co rrectly? If not please indicate where correction or revision is needed.B-4 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE 

# Agenda (cont’d.)

12:00 PM LUNCH (on your own)

1:15 PM Charge Question 2 (discussion continues) ........................................ Walter Do dds ( **Chair) & Reviewers**

1:45 PM Charge Question 3

................................................. ............................ **Walter Dodds (Chair) & Reviewers**

This report concludes that for non-riparian/non-flo odplain wetlands that are not connected to the river network through a stream channel (i.e., geogra phically isolated wetlands and wetlands that spill into losing streams), connectivity and isolat ion vary within a watershed and over time, making it difficult to generalize about their connections to, or isolation from, downstream waters. The literature we reviewed does not provide sufficient information to evaluate the degree of connectivity (absolute or relative) of these non-ri parian particular wetlands. a) Are these conclusions supported by the scientific e vidence? b) Does the report include the most relevant peer-revi ewed literature on these topics, including evidence of connectivity **and** isolation? If not please indicate which references are missing. c) Was the reviewed literature cited and summarized co rrectly? If not please indicate where correction or revision is needed.

3:15 PM BREAK

3:30 PM Charge Question 4

................................................. ............................ **Walter Dodds (Chair) & Reviewers** This report concludes that while the influence of a particular stream or wetland on downstream waters might be small, the aggregate contribution b y an entire class of streams or wetlands (e.g., all ephemeral streams in the river network, or a clu ster of small wetlands) might be substantial. a) Is this conclusion supported by the scientific evid ence? b) Does the report include the most relevant peer-revi ewed literature on this topic? If not please indicate which references are missing. c) Was the reviewed literature cited and summarized co rrectly? If not please indicate where correction or revision is needed.

4:15 PM Review of Discussion Highlights

.................................................. ..... **Walter Dodds (Chair) & Reviewers**

5:15 PM Closing Remarks

.................................................. ................................................... ............... **Kate Schalk**

5:30 PM ADJOURNC-1 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE



## Appendix C: List of ReviewersC-1 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE United States Environmental Protection Agency National Center for Environmental Assessment 

# Peer Review Meeting for EPA’s Draft Report: Connect ivity of Streams and Wetlands to Downstream Waters - A Re view and Synthesis of the Scientific Evidence

Hilton Garden Inn –Downtown Washington, DC January 30, 2012 

# Peer Reviewers

David J. Cooper, Ph.D. Senior Research Scientist and Professor Department of Forest and Rangeland Stewardship Colorado State University Fort Collins, CO
William G. Crumpton, Ph.D. Associate Professor Department of Ecology, Evolution & Organismal Biology Iowa State University Ames, IA

Kenneth W. Cummins, Ph.D. Adjunct Professor Department of Fisheries Biology Humbolt State University Arcata, CA

Walter K. Dodds, Ph.D. **(Panel Chair)** University Distinguished Professor Division of Biology Kansas State University Manhattan, KS
James W. La Baugh, Ph.D. Hydrologist Office of Groundwater U.S. Geological Survey Reston, VA

Mark C. Rains, Ph.D. Associate Professor Department of Geology University of South Florida Tampa, FL John S. Richardson, Ph.D. Professor Department of Forest Sciences University of British Columbia Vancouver, BC, Canada
Joel W. Snodgrass, Ph.D. Chair, Department of Biological Sciences Towson University Towson, MD
Arnold van der Valk, Ph.D. Professor Department of Ecology, Evolution & Organismal Biology Iowa State University Ames, IA
Mark S. Wipfli, Ph.D. Professor Cooperative Fish & Wildlife Research Unit U.S. Geological Survey Fairbanks, AK

William R. Wise, Ph.D. (Unable to Participate in Meeting) Associate Professor Department of Environmental Engineering Sciences University of Florida Gainesville , FLD-1 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE



## Appendix D: List of ObserversD-3 I NTERNAL D ELIBERATIVE M ATERIALS : D O N OT D ISTRIBUTE , Q UOTE , OR C ITE United States Environmental Protection Agency National Center for Environmental Assessment 

# List of Observers

EPA
Rebecca Aicher, AAAS Fellow, U.S. Environmental Pro tection Agency, Washington, DC Laurie Alexander, U.S. Environmental Protection Age ncy, Washington, DC Donna Downing, U.S. Environmental Protection Agency , Washington, DC Rachel Fertik, U.S. Environmental Protection Agency , Washington, DC Scot Hagerthey, U.S. Environmental Protection Agenc y, Washington, DC Rose Kwok, U.S. Environmental Protection Agency, Wa shington, DC Stephen LeDuc, U.S. Environmental Protection Agency , Washington, DC Jim Pendergast, U.S. Environmental Protection Agenc y, Washington, DC Amina Pollard, U.S. Environmental Protection Agency , Washington, DC Hadas Raanan-Kiperwas, ORISE Fellow, U.S. Environme ntal Protection Agency, Washington, DC Caroline Ridley, U.S. Environmental Protection Agen cy, Washington, DC Mark Ryan, U.S. Environmental Protection Agency, Bo ise, ID Kate Schofield, U.S. Environmental Protection Agenc y, Washington, DC Michael Slimak, U.S. Environmental Protection Agenc y, Washington, DC



## USACE David Lekson, U.S. Army Corps of Engineers, Wilming ton, NC Robert Lichvar, U.S. Army Corps of Engineers, Hanov er, NH Karen Mulligan, U.S. Army Corps of Engineers, Washi ngton, DC



## EPA – VIA TELECONFERENCE Ken Fritz, U.S. Environmental Protection Agency, Ci ncinnati, OH William Kepner, U.S. Environmental Protection Agenc y, Las Vegas, NV Charles Lane, U.S. Environmental Protection Agency, Cincinnati, OH Michael McManus, U.S. Environmental Protection Agen cy, Cincinnati, OH Scott Leibowitz, U.S. Environmental Protection Agen cy, Corvallis, OR Jim Wigington, U.S. Environmental Protection Agency , Corvallis, OR



## USACE – VIA TELECONFERENCE Sally Yost, U.S. Army Corps of Engineers, Vicksburg , MS Dan Smith, U.S. Army Corps of Engineers, Vicksburg, MS