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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, 2012 

 

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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 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 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 literature on these topics, including 

evidence of connectivity and isolation? If not please indicate which references are missing. ...... 17

c) Was the reviewed literature cited and summarized correctly? If not please indicate where 

correction or revision is needed. ................................................................................................ 24

2. This report concludes that open water and wetlands in riparian areas and floodplains of streams 

and rivers are physically, chemically, and biologically connected with the river network, and 

that their functions exert a strong influence on the character 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 literature on these topics, including 

evidence of connectivity and isolation? If not please indicate which references are missing. ...... 30

c) Was the reviewed literature cited and summarized correctly? If not please indicate where 

correction or revision is needed. ................................................................................................ 32

3. This report concludes that for non-riparian/non-floodplain wetlands that are not connected to 

the river network through a stream channel (i.e., geographically 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 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. ................... 34

a) Are these conclusions supported by the scientific evidence? ...................................................... 34

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. ...... 43

c) Was the reviewed literature cited and summarized correctly? If not please indicate where 

correction or revision is needed. ................................................................................................ 44
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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. ..... 46

a) Is this conclusion supported by the scientific evidence? ............................................................. 46

b) Does the report include the most relevant peer-reviewed literature on this topic? If not please 

indicate which references are missing. ....................................................................................... 48

c) Was the reviewed literature cited and summarized correctly? 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-1
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Introduction 

The U.S. Environmental Protection Agency’s (EPA’s) National 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 identifying 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 nationally 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 Florida1

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 convened 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 attend. 

The meeting was closed to the public and considered an internal EPA deliberative process. Observers from 

EPA and the U.S. Army Corps of Engineers attended to listen 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 the 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 this report. These comments reflect the individual 

opinions of the reviewers. 

 

1 Since Dr. Wise was unable to attend the workshop, only his pre-meeting comments are included. 

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Reviewers’ Highlights from Meeting Discussions 

Peer Review Meeting for EPA Draft Report: 

Connectivity of Streams and Wetlands to Downstream Waters - A Review 

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 technical 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 influence 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 strong for some wetland types but many are strongly 

connected to downstream waters. The introduction needs an overarching spatial and temporal conceptual 

model of the gradients of connectivity across landscapes, and 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 reviewed 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 considered in the introduction and the individual 

chapters (or in its own chapter), and such consideration should 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. 

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Post-Meeting Responses to Charge Questions 

Responses to Charge Questions 

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Introductory Comments (Not all reviewers provided introductory comments.) 

Reviewer Comments 

Cooper The authors of the report have done an excellent job of bringing 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 review indicates that our knowledge of hydrologic connections 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 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 each section of the report must 

have a discussion of what is unknown or uncertainties about connections, functions, and 

what future research is needed to support our understand of these processes. The report 

gives the impression that we know most of what is needed to understand and regulate these 

tributaries and wetlands. I think this is only partially correct. 

The temporal aspect of these jurisdictional identifications 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 is 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 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 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 

Evaluation Technique, HGM and other approaches that all have been extensively peer 

reviewed and used in the U.S. I include a few key references at the end of my comments. 

Methods such as these are critical for inclusion because any 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 situated waters” as a way of 

extending our understanding beyond single sites. However, the geomorphic context of such 

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 improvement. For example wetlands, 

riparian, floodplain, non-riparian wetland, etc. are all in 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 used as these definitions have been 
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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 areas 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 Pedro river is not a representative 

stream. Much attention has been paid to the San Pedro, making 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 most has well developed riparian 

forests. In contrast most 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 and 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, and functions that effect downstream 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 within could also provide a good 

framework for discussing issues related to connectivity, and uncertainty in connections and 

ecological functions. Another potential is to organize around HGM wetland types, such as 

depression, slope, etc. although there is great variance through the U.S. on how 

basin/depression wetland function. 

Beavers are a key part of the biotic/hydrologic connection for 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 important 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 the landscape is connected to the 

channels. 
Responses to Charge Questions 

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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 water 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 showing 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 published sources of 

information. I particularly like the framework of source, sink, refuge, transformation and 

lag to identify key functions. This approach really allows the issue at hand to be very 

clearly explored. However, this framework is not really clearly delineated throughout the 

document, and I think the document would be strengthened 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 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, 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 questioned 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, transformation 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 

framework doesn’t seem to be used throughout the stream examples (chapter 4). For 

instance, the example from the prairie streams doesn’t mention these conceptual 

components much. The examples given about streams provide good examples 

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 definition of 

riparian area as transitional between aquatic and terrestrial (P.26) makes it difficult to know 

when 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, 
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unless this simply means not in the riparian area of a navigable-in-principle stream. The 

consistent use of floodplain and riparian as a combination term (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 floodplain 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 explained 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 navigable-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 material on P.136-137 contributes to the 

understanding of whether this is a navigable-in-principle stream 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 with that. 

It appeared to me that the Executive Summary was a little 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 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 opinion(s) should be explained a little 

further. 

I like the idea of proportional benefits from non-navigable waters, as expressed in the 

Leibowitz et al. (2008) paper. Moreover, the idea that these benefits may be realized or 

potential benefits is a helpful way to think about the capacity of a source system to provide 

benefit. However, 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 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 trying 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 staff, 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 
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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 subfamily 
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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 and functioning of downstream 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 to a water of the U.S. on some time 

scale, likely years to decades. 

Crumpton The conclusion that all streams are physically and chemically 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 streams 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 excluding certain channel origin wetlands 

that feed losing streams. The exception of certain wetlands spilling to losing streams as 

potentially not being connected to downstream 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 lack a connection to downstream 

waters, the conclusion that at least collectively streams exert a strong influence on the 

character and function of downstream waters is well supported. The report illustrates this 

through estimates of the fractions of river flow and material loads (nutrients, carbon, etc.) 

that originate in streams. 

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 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 appropriately. The report does a 

particularly good job in summarizing the complex nature of stream 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. 
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Cummins The conclusions are supported by the scientific evidence. 

Dodds For the most part, these conclusions are supported by the scientific 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 essential suggestions. 

The general synthesis of the cited literature provided in the report supports conclusion 1. 

The document, however, includes some conceptual inconsistencies 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 interaction with the wetland is 

remarkable. The fact there are local, intermediate, and regional flow systems is 

illustrated by Toth’s work [see figure A-4 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 representing 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 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 alluvial 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 

formation 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...” is 

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 sufficient saturated permeable 

material to conduct ground water and to yield economically significant 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.; or “An 
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aquifer is a formation, group of formations, or part of a formation that contains 

sufficient saturated permeable material to yield significant quantities of water to wells or 

springs.” S. W. Lohman and others, 1972, Definitions of selected 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 the 

key points being made about flow systems while being consistent with correct use of 

technical terms. It is not at all clear why the explanation includes reference to 

intermediate 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 from beyond 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 deleting 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 some flaws and/or 

inadequacies in the 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. 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. 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 

provide clearly articulated evidence, one way or another, toward connectivity in these 

contexts to better enable decision-makers to resolve this policy 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 and ecological connectivity are 

central tenets of stream hydrology and ecology. Some examples might include the Four-
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Dimensional Nature of Lotic Ecosystems (Ward 1989), the River Continuum Concept 

(Vannote et al., 1980), the Serial Discontinuity Concept (Stanford et al., 1988, Ward and 

Stanford 1995, Stanford and Ward 2001), and the Featured Collection of JAWRA devoted 

to this very topic (Nadeau and Rains 2007 and references therein; Note: 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 accepted hydrological and ecological 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 paragraph. 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 explain reach-scale flowsediment dynamics. Because Lane (1955) is often difficult to track down, you might also 

cite Bull (1991), who republished the findings of Lane (1955). 

l. 1977-1978: The following two comments relate to nutrient subsidies, 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 

consider the following two comments here or elsewhere in a separate 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 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 mineralized, and 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., March–April). Thus, during the 

early-season storm events, there is little biological demand for nitrate and it is readily 

leached from the upland 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-fixed nitrogen 

subsidies in wetlands and streams. For example, Shaftel et 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 all 
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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 might 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. Also, Hill and Lymburner (1998) and 

Hill et al. (1998) did nice studies on nitrogen transformations in hyporheic zones, showing 

that even short, shallow, and fast flowpaths through the hyporheic 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 toward the receiving water bodies (e.g., 

the ocean). Nutrient spiraling is a way by which those nutrients 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 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 that 

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 importance of 

anadramous fish in transporting nutrients, especially marine-derived nutrients, to 

headwater streams and associated riparian habitats. There is a good review of this in 

Nadeau and Rains (2007). 

l. 2486-2487: You might also consider adding a paragraph here on barriers 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 

Soviet Union are fragmented by dams and/or significant water 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 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. 

Richardson Yes, the conclusions are consistent with the evidence presented in the scientific, peerreviewed literature. 
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Snodgrass Yes, the scientific evidence clearly indicates a significant 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. 

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

the literature cited. 

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

the scientific literature. There is strong evidence in the scientific literature that headwaters 

are physically, biologically, and chemically connected to, and 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 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 

loops, the unidirectional flow of streams creates open cycles 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 hydrology 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 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 suggested using airshed, watershed, and ground-watershed to categorize all the approximately 

definable inputs and cycles with in a region. 
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23 509-10 Headwater streams are first- and second-order streams... I feel strongly 

that alternatives to this statement should be acknowledged. For example, 

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 orders 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 in most 

headwater streams. 

 Here, and elsewhere, the point should be driven home that stream order is a 

geomorphic concept and probably never should be inferred from blue 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., California Forest 

Practices Rules, Section 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 

spawning. 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. Class 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 access roads) “and are 

capable of sediment transport to Class I and II waters under normal high 

water flow conditions. (Cummins, K. W. and M. A. Wilzbach. 2005. The 

inadequacy of the fish-bearing criterion for stream management. Aquatic 

Sciences. On line; http://www.birkhauser.ch, pp 1-6). 

24 531 ...symmetry ratio... another way is link number, which sums the total 

number of first-order tributaries entering a watershed of a given order. Fig. 

3-1 shows no first-order tributaries entering directly into the third-order 

mainstem which would be quite unusual. Link number is a useful measurer 

for stream ecologists working at the watershed scale because 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 indication 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 height in the riparian 

area. The point that needs to be acknowledged (driven home), is that 

stream ecologists, fisheries managers, and forestry managers all have 

different concepts (or biases) about the definition of the width. For 

example, stream ecologists may focus on the width necessary to provide 

the width that supplies plant litter that constitutes the primary energy 

source of headwater stream ecosystems, fisheries managers are concerned 

with the width necessary to insure the input of large wood which is the 
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mainstay 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 defining 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 with a dashed line at 

the ends. The figure caption should explain that the dash lines 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 particulate organic 

matter (FPOM, particle size < 1mm) and is taken up directly by benthic 

bacteria. This significantly delays the export of organic matter down river. 

DOM almost universally accounts for 50% of all the organic matter in 

transport in all order streams (Vannote et al., 1980 and the Minshall et al., 

River Continuum publications). This retention of FPOM, rather than loss 

as DOM, has major consequences for stream and river invertebrates 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 intervals involve flows 

too small to cause significant changes in stream channel geomorphology, 

and very long recurrence intervals cause very major alterations in channel 

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 forest landscapes. Pp. 91-138 in: Salo, E. 

O. and T. W. Cundy. (eds.). Streamside management: forestry and fisheries 

interactions. Institute of Forest Resources, Univ. Washington, 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 America, Central and 

south America, Europe, Africa, Asia, Australia and New Zealand, 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 editors presents an overview of 

stream ecosystems. The River Continuum Conceptual Model (Vannote et 

al., 1980) is reproduced in the Introduction. This is the model that relates 

stream/river ecological structure and function to the position along the 

downstream trajectory. (Cushing, C. E., K. W. Cummins, and G. W. 

Minshall. 2006. River and stream ecosystems of the world. Univ. 
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California Press, Berkeley 817 p.) 

110 2145 ...108 m for whole leaves... This compares to the 100 m in Cummins et al. 

(1989) and not to the 1000 m cited in this report. 

112 2197 ...snow melt. Approximately 50% of transported carbon was DOC 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 anaerobic storage of 

CPOM, e.g., leaf litter, greatly delays breakdown of CPOM to FPOM in 

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, DC Mahan, and R.L. Mattingly. 

1980. Processing of confined and naturally entrained leaf litter in a 

woodland stream ecosystem. Limnol. Oceanogr. 25:952-957.] 

120 2382 Wilzbach and Cummins (1989) demonstrated a higher % mortality among 

drifting individuals than their benthic counterparts. This raises the 

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 the contribution being to the downstream detrital 

suspended load. (Wilzbach, M. A. and K. W. Cummins. 1989. An

assessment of short-term depletion of stream macrobenthos 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. 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 majority of 

introduced leaf litter in a forested second-order stream by reported to be 

about 100 m by Cummins et al. (1989). [Travel distance of leaf litter was 

reported from the time the litter is wetted. Senescent Ginkgo leaves were 

used in these 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 the native riparian tree species in eastern 

headwater streams.] 

Attached is a figure that might be of interest to some people at the meeting. I make no 

suggestion whatsoever that this Figure should be any part of the report. It is merely a “snap 

shot” offered in support of the argument that I did make in the report about including 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 first- to third-order). The photograph is not unique; this sort of 
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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, Oregon, New Mexico, 

Yellowstone Park (Wyoming and Montana), Idaho, Michigan, Pennsylvania, Maryland, 

Florida, Sweden, Denmark, Italy, Australia, New Zealand, Brazil, and Guinea West Africa. 

Fig. A. Conditioned red alder leaf eaten by caddisfly (Trichoptera) larvae. Note: better conditioned (higher aquatic 

hyphomycete fungal biomass) soft tissues eaten in preference to the poorly conditioned midrib and major 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 Technical 

Charge Question 1. 

So, as I argued in one of my comments in Response to Charge question 1, this world wide 

and highly predictable connection between riparian vegetation and 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 references 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. 
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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. Streams 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 forested 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, some species of stream-side 

salamanders are headwater specialist, which are only found in large numbers in headwater 

streams (Snodgrass et al., 2007; Peterman et al., 2009). Headwater specialists often have 

adaptations that allow them to cope with desiccating conditions 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 important component of protecting the 

biodiversity associated with our nation’s waters. The authors do acknowledge 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 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 headwater 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; Butler and Malanson, 

2005) and provide habitat for numerous organisms (e.g., Snodgrass and Meffe 1996; 

Stevens et al., 2006). These hydrological and geomorphological changes have large 

impacts on ecosystem function (Naiman et al., 1996) including 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 headwater 

streams being places of lag and transformation. This material 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 streams (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% 
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of 400.3 km of stream did not show up as blue lines on 1:25,000 scale USGS topographic 

maps. There is also 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) later the authors suggest that headwater stream originate at 

where “runoff is sufficiently concentrated to erode a definable 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 channel. 

On lines 3399 through 3413 the authors summarize the effects of altered 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 species. Again, this is a place to integrate 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 rivers. 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 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 biological linkages that may be 

helpful are listed below. The latter four deal with management effects on headwater 

streams. 

Wipfli, M.S., and C.V. Baxter. 2010. Linking ecosystems, food 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 detritus transport 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 influence 

logging effects on benthic communities? Hydrobiologia 641: 71-83. Addresses past 

timber harvest effects on headwater stream invertebrate communities.

Wipfli, M.S. and J. Musslewhite. 2004. Density of red alder (Alnus rubra) in headwaters 

influences invertebrate and organic matter subsidies to downstream fish habitats in 

Alaska. Hydrobiologia. 520: 153-163. This paper showed that headwater streams 
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also supply terrestrial invertebrates to downstream waters, in addition to aquatic 

invertebrates, and illustrated 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 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 streams 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. Freshwater Biology 

53: 2331–2343. 

c) Was the reviewed literature cited and summarized correctly? If not please 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 correctly. 

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

is one reference that is cited, Dodds and Oakes 2006, which indicates 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 reaches as well, 

although figure 3-13 helps. Also a figure with a longitudinal cross 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 it looks like everything flows into 

everything else through the river. 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 figure 3-14 is somewhat misleading as it ignores 

cycling through inorganic forms. 

Line 1031, these streams flow during and immediately following precipitation. 
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A clearer discussion of when increased connectivity can be bad (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 change longitudinal patterns, 

but much less severely and in very different ways from dams. 

Line 1793. In the Flint Hills of Kansas, wood does not accumulate in small streams, and 

such streams are an important source of large wood to downstream rivers. This wood is 

very important habitat as well as a geomorphologic force in rivers. This statement might 

need to be qualified a bit. 

Line 2495, might want to discuss the Falke and Gido 2006 (in references) work here on 

reservoirs disconnecting small streams from each other. 

Line 2560. This could be stated more strongly. The evidence unequivocally 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., 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 ecoregions, 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 establishing reference 

nutrient concentrations across watersheds affected by humans. Limnology and 

Oceanography Methods, 2, 333-341. 

Line 2750, these are still net heterotrophic, so they are derived 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 citation 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 and covers the evidence for 

connections. Yes, the conclusions are supported and appropriate literature is compiled. 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 
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streams are connected to rivers might be in the case of coastal 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 authors 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 streams. See discussion above 

for references. This change should be made in the final document. 

van der Valk I am not an expert on 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 summarized 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 examples) 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 from 

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. 
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2. This report concludes that open water and wetlands in riparian areas and floodplains of 

streams and rivers are physically, chemically, and biologically connected with the river 

network, and that their functions exert a strong influence on the character 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 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. 

Crumpton The conclusion that wetlands in riparian areas and floodplains 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 riparian areas and 

floodplains of certain permanently losing steams that are never connected to downstream 

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 migration of organisms. 

The conclusion that wetlands in riparian areas and floodplains of streams and rivers exert a 

strong influence on the character and function of downstream waters is well supported by 

the scientific evidence – at least for the systems collectively, and that 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 the 

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 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, as 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 are areas where groundwater 

flows to the wetlands rather than the adjacent river, thereby intercepting groundwater 

that otherwise would contribute to baseflow? 
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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 regarding some flaws and/or 

inadequacies in the 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: The classification scheme used in this document is unusual. I 

understand why you might want to separate this into channels, wetlands on floodplains, 

and wetlands not on floodplains, given the regulatory environment. 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 might then explain what kinds 

of wetlands might be included, using an HGM classification scheme. In this way, you can 

explain that this chapter is dealing with all kinds of wetlands—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 and ecological connectivity are 

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 floodplains (Ward and Stanford 1995). Doing so will 

accomplish two objectives: (1) make it clear from the outset 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 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 floodplain wetlands. However, it 

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 sediments. Riparian areas provide 

both short- and long-term storage locations for sediments, 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 mobilization balance; accommodation 

space has been created—in which case, sediments can be stored; or accommodation space 

has been destroyed—in which case, sediments can be mobilized (Quirk 1996). 
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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 better 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 discharges to riparian 

environments flows along regional groundwater flowpaths, and is therefore 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 evapotranspiration causes water levels 

to rise. The paper, in my opinion, is a bit flawed, in that 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 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. 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 water table up toward the 

point. (This, in fact, is the source of the well-known capillary fringe.) The point may not be 

saturated—in fact, in most alluvial deposits, the point will 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, which 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. (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 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 referenced 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 agricultural runoff (Peterjohn and Correll 

1984), the roles played by hyporheic flows, including those at the 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-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 et 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. 
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Snodgrass On lines 233 and 234 the authors suggest that riparian buffer zones 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 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 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, biological) between rivers and 

floodplain wetlands were well documented. 

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

the scientific literature. There is strong evidence in the 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 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 2a) above. 

Crumpton See comment 2a) above. 

Cummins 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 headwater streams 

are not the initial source of river networks should be flagged. For example, 

the Yellowstone River (one of the longest and largest un-dammed rivers 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-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 26, 559, 

there is little agreement about this, because the width is dependent upon 

the function being considered or the management objectives dependent 

upon the width as define by regulations. For example, foresters interested 

in timber harvest will argue for the smallest width possible while fisheries 

managers will argue for a width sufficient to provide recruitment of LWD. 
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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 between the riparian 

zone and the adjacent aquatic system and, therefore, the connectivity 

downstream is that the plant species composition of the riparian 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). This 

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. The 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 cited. 

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

Rains See comment 2a) above. 

Richardson The literature covered is excellent. 

Snodgrass To the best of my knowledge in this area the report does include 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 unequivocal 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 rivers and floodplains like Amoros and Bornette (2002). Again, I 

doubt that the conclusions drawn from the literature reviewed would be affected in any 

way because some relevant references were not included. 

Some relevant papers from outside NA that are missing include: 

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.
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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. Ecological 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. Extreme flooding events on the 

Rhine and the survival and distribution of riparian plant species. Journal of Ecology 

91: 135-146. 

Wipfli Yes, the report appears to include the most relevant literature 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 please 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 riparian 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 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: 

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-river wetlands. Bioscience,

48, 721-733. 

b. Galat, D.L. & Lopkin, R. (2000) Restoring ecological integrity of great rivers: 

historical hydrographs aid in defining reference conditions for the Missouri River. 

Hydrobiologia, 422/423, 29-48. 
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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 restoration 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 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. 

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 connections. 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 floodplain differed from a riparian area, so 

to refer to “riparian and floodplain” wetlands seems redundant (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 this should be defined as a nonfloodplain wetland. 

Snodgrass To the best of my knowledge in this area the report does correctly 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 summarized thoroughly and correctly. 
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3. This report concludes that for non-riparian/non-floodplain wetlands that are not connected to 

the river network through a stream channel (i.e., geographically 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 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? 

Reviewer Comments 

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

wetlands to streams is sparse, and the conditions for such 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 wetlands that are not 

connected to the river network through a stream channel, connectivity and isolation varies 

within a watershed and over time is well supported by the scientific evidence. 

The conclusion that the literature reviewed does not provide sufficient 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 downstream waters. The report should 

attempt to provide guidance on how to distinguish these two categories (perhaps using 

soils and other indicators). The report distinguishes geographically 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 illustrated 

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 isolated wetlands since swales can be 

“upland”. However, it would also include in this category prairie pothole depressions that 

spill over onto wetland flats or slope wetlands rather than to a channel. Wetland 

depressions that spill over to wetland systems (including wetland 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 truly geographically isolated. 

The report provides reasonable coverage of the relevant peer-reviewed literature on 

connection and isolation of non-riparian/non-floodplain wetlands to the downstream 

waters but does fall short in a few areas. 
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The report fails to adequately address the effect of subsurface 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 example lines 5166-5170 on pages 249-250 of section 5.8.3.1). The report states 

that “When potholes are artificially connected to streams and lakes though drainage, 

isolation is eliminated and they 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 is given to the importance of 

subsurface “tile” drainage which is ubiquitous throughout the Corn Belt and many 

other areas. The report mentions only briefly that “drains fitted at the bottom of 

potholes connected to shallow subsurface pipes often discharge to 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 to downstream waters. 

Specifically, do surface intakes of subsurface drainage pipes (“tile drains”) provide a 

direct connection to downstream waters for what might otherwise be considered 

geographically isolated wetlands? 

The report in part uses HGM (hydrogeomorphic) wetland classification and could 

benefit from a review of the wetland classes in this system. Important 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 these landscapes. 

The report should also provide information on the relationship 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 isolated 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 surface outflow and connectivity 

is expected in wetter portions of the prairie pothole but extends 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). 
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A broader analysis of this pattern for the Prairie Pothole is provided by Johnson et al. 

(2005. Vulnerability of northern prairie wetlands to climate change. Bioscience 55: 

863-873). Their models of wetland water regimes suggest that spillover to downstream 

waters is a common occurrence in the wetter portions 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 flow 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 between the more interconnected wetlands 

of the Des Moines Lobe and the more isolated wetlands of the drier portions of the 

Prairie Pothole Region. 

The literature is for the most part cited and summarized correctly. However, in several 

places (line 1435-1468 and others), the report incorrectly describes the subregions of the 

Prairie Pothole Region, essentially ignoring the Des Moines lobe. This is the southeastern 

and wettest portion of the Prairie Pothole and as suggested above, its wetlands might be 

expected to have greater connectivity to downstream waters. 

Cummins The conclusions are supported by the scientific evidence. 

In general they are supported by the literature cited. However, 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 about a reorganization of the 

information that was presented in the Document. I think the general thrust of the 

recommendation would improve the Document and not require much, if anything, in the 

way of new information. 
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The organization would not be levels of connectivity but rather functional classes of 

connectivity: hydrologic, physical (geomorphic), chemical (nutrients/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 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 streams and 

wetlands of various types are, the lower probability they will exhibit high connectivity on 

any time scale. 

This more functional approach would provide, I believe, a better 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 biological isolation, because 

migrations will always bridge hydrologic, physical, and chemical isolation. 

Dodds 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 other waters, then the only 

output of water must be evaporation. If this is the case then 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 connected to downstream waters 

either directly or through groundwater. 

La Baugh The overall synthesis of the cited literature provided in the 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 and hydrological 

isolation? The issue of connectivity would seem to be a function 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, lines 340 to 342. Why 

is the non-channelized swale considered to be upland? By the definition on page 15, 

the wetland is geographically isolated when completely surrounded 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 geological 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 groundwater? What about the 
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importance of topographic setting with respect to the presence 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-riparian wetland with 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 particle 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 high- permeability terrain in comparison with those in lowpermeability 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 lowpermeability terrain. 

• Page 250, line 5175 – One factor that can change the chemical characteristic of prairie 

pothole wetlands is loss of sediment due to wind erosion during periods 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 

prairie pothole wetlands and streams or river networks is the presence 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 streams 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 what 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 transporting 

sediment or chemicals to streams.
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• 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 lowpermeability substrates rather than impermeable substrates. Also, if the substrate is 

impermeable, by definition it will not contain a surficial aquifer. A low-permeable 

substrate could contain a shallow groundwater system separated 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 well 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 ecological connectivity are not 

fundamental tenets for these systems. However, I do have comments regarding some flaws 

and/or inadequacies 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 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 Rains (2011), who showed that 

moraine, ice-scour, and dead-ice depressional wetlands serve as groundwater recharge 

focal points because aeolian-transported snow is trapped in the topographic lows in winter 

and then melts and recharges underlying groundwater immediately following breakup in 

late spring, with the net effect being that groundwater recharge 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 important case of 

groundwater flow-through wetlands. Groundwater flow-through lakes and depressional 

wetlands, where surface waters are a surface expression of broader groundwater 

phenomena, have long been recognized. Born et al. (1979) and Rains (2011) described 

groundwater flow-though depressional wetlands in glaciated landscapes, Sloan (1972) and 

Richardson et al. (1992) described groundwater flow-through prairie potholes in the 

northern prairie, and Murphy et al. (2008) described groundwater flow-through 

depressional wetlands in clay-rich soils with abundant desiccation 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 seasonal perched aquifer 

that is unconnected to the underlying regional aquifers. 
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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 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-season baseflow ceased 

earlier when an incised river was restored to the historic floodplain. One 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 connections to 

one another and to nearby streams. 

l. 4401-4402, l. 4415-4425: I lump these specific lines together in one comment to make 

an important point. In the first case, you state in clear, concise, and unequivocal terms that 

riparian and floodplain wetlands are highly connected to river 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 systems under certain circumstances. 

You are correct; however, by dithering and then only vaguely supporting the idea that nonriparian and channel origin wetlands might be connected to river systems, and then only 

under certain circumstances, I think that you soft-peddle what we know about the flow of 

water across landscapes. To be honest, all hydrologic systems are interconnected to some 

degree 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 where we might choose to 

transition from their being a significant nexus to their not being 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 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 references at the end of 

this sentence. 

l. 5385-5387: You might consider adding Rains et al. (2006) to the references 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 perched surface-water systems; the 
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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? 

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 categorically conclude that this class 

of wetlands is connected. The role of isolated wetlands in 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. Likewise, the contributions of 

these isolated wetlands on transformation and storage of nutrients, 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 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 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 streams are widespread and high 

rates of a number of ecological processes have been measured; therefore, these systems 

must have an impact on downstream rivers. In fact, this is a general approach that 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 extensive coverage of geographically isolated wetlands—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 address this issue, I think 

the argument could be made more forcefully. In fact, what 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 wetlands 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 large impacts on streams, stream 

hydrology, geomorphology, ecosystem function, and biological communities, ultimately 

affecting downstream rivers (Paul and 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 no 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 wetlands have a 

disproportionally large influence on downstream waters compared to upland habitat loss. 

Therefore, 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 downstream streams and rivers is stronger than the authors indicate 

with this conclusion. See my general post meeting comments for further discussion of this 

issue. 
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The authors discuss “isolated wetlands that have no hydrological 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 connection to 

ground waters (either through recharge or discharge and recharge). If such studies exist 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 deep 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 groundwater 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 and 

similar to geographically isolated wetlands. 

Also related to the above comments, in the case study of Carolina bays the authors suggest 

that groundwater and surface water connections of bays to streams 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 other 

downstream waters.” Later (on lines 4097-4098) the authors indicate wetlands that feed 

losing streams cannot be considered channel wetlands. However, 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 hydrological connectivity to 

rivers could ever be drawn for the entire category. There are situations where 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 types of wetlands are connected biologically to rivers and vice versa in 

many, if not all, cases. 

Wipfli Question is outside my area of expertise. 
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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 literature on those topics, including 

evidence of connectivity and isolation as presented. However, if a different organization of 

the report is adopted, as discussed above, a reorganization 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 connections in the Highland Lake 

District of Wisconsin, and these connections include wetlands. 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 productivity, Trout Lake watershed, 

northern Wisconsin, USA. Journal of Hydrology, 320, 370-384. 

There is a huge amount of work on hydrologic and chemical connection 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 inconsistent 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 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 flow in a variety of landscapes is 

Richardson, J.L., and Vepraskas, M.J., editors, 2001, Wetland soils: genesis, hydrology, 

landscapes, and classification. Lewis Publishers, Boca Raton, Florida, 417 p. 

• Page 283, lines 6053 to 6056 – Entry for the cited literature source is not complete 

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 complete 

regarding the publication information. 
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The correct entry for the Vining 2002 should be revised as follows – 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 follows 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/

Rains See comment 3a) above. 

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

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

communities also applies to geographically isolated wetlands. As the authors 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 

have large effects on wetland communities through predation, and trade-offs among the 

competing demands of surviving desiccating conditions and predation pressures creates 

adaptations to narrow ranges of hydrological and predator community 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 alter biodiversity associated with 

isolated wetlands. See Snodgrass et al. (2000) for further discussion 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 literature on “clusters” of wetlands. 

Although wetlands within a cluster evidently are linked, presumably by groundwater flows, 

they are 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 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 hummocky terrain. 

Wipfli Question is outside my area of expertise. 

c) Was the reviewed literature cited and summarized correctly? If not please 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. 
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Dodds Yes, this is cited and summarized correctly. 

Line 5177 the word detrimental is loaded, if it is a natural 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 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 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 wetlands was summarized correctly. 

Rains See comment 3a) above. 

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

the collective evidence. 

Snodgrass The literature that was reviewed appears to be interpreted 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 wetlands to rivers by groundwater 

flow is largely ignored. 

Wipfli Question is outside my area of expertise. 
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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 evidence? 

Reviewer Comments 

Cooper The contribution of streams and wetlands on downstream waters is well known for flood 

water retention (the studies by Novitski 1978 in Wisconsin should 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 influence of an individual stream 

or wetland might be small is clearly supported by the scientific evidence (and by simple 

common 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 in the treatments of 

streams, riparian/floodplain wetlands, and non-riparian/non-floodplain wetlands. 

The literature relevant to this topic was cited and summarized appropriately although its 

dispersion throughout the document makes it less easily accessible 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. This point is actually true for any nonpoint pollution source, and the entire field of watershed management 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. 

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

conclusion noted as 4 above was not presented. Nor was a fourth 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 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 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 streams in the watershed will have a measurable and 
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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 Preston 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 

between all of the disparate pieces separately discussed in this 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 example, you do discuss the 

role that depressional wetlands play in storing water and 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 flood 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 typically have a step when a storm begins where rainfall is 

abstracted and put into depressional storage 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 occurring 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 and 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 case for moraine, ice-scour, and 

dead-ice depression in southwest Alaska. He did not 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 wetlands in these environments, implying that, 

though the individual effect of one wetland may be negligible, the 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 navigable 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 wetlands and streams (if not all) make 

substantial contributions to the structure and functioning of downstream waters. 
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van der Valk For streams, this conclusion is self-evident and is supported 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 exactly 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 downstream waterways that 

unfortunately can easily be overlooked, and I was pleased to see this addressed. 

Individually, small streams do generally not have large influences by themselves on 

downstream processes, but in aggregate they tremendously affect 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 literature 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 transfer 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 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 intermediate 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 concluded 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 relevant 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 some putatively isolated 
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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 literature on the cumulative effects of 

headwaters. 

c) Was the reviewed literature cited and summarized correctly? If not please 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 correctly, or relevant comments were 

covered under the first three Charge Questions (e.g., comments about adaptations by 

invertebrate life cycles to accommodate periodic drying, in which the annual predictable 

seasonal flows of intermittent streams have more taxa adapted to the condition than in 

ephemeral streams, in which annual flows can only be described 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 literature 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 literature 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. 

Wipfli Yes, to the best of my knowledge the literature on this topic was cited and summarized 

thoroughly and correctly. 

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Additional Reviewer Comments 

David J. Cooper, Ph.D. 

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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). Wetland functions and values: the status of our 

understanding. Proc. National Symposium on Wetlands. Am Water Res Assoc, Minneapolis MN. 

Thomas C. Winter, Judson W. Harvey, O. Lehn Franke, William 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 Assessing the Functions of Riverine 

Floodplain Wetlands in the Northern Rocky Mountains. Special 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 wetlands in the northern Rocky Mountains. 

Special Publ. WES, USCOE, Vicksburg, MS. p.189. 

THREE papers (PDFs provided) that you might consider referencing as they present original data on 

hydrologic connectivity on ephemeral and intermittent streams to riparian and wetland ecosystems 

Shaw, J. and Cooper. D.J. 2008. Watershed and stream reach 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. Stream/aquifer interactions at Great Sand Dunes 

National Monument, Colorado: Influences on interdunal wetland disappearance. Journal of Hydrology

271:77-100. 

William G. Crumpton, Ph.D. 

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Additional Comments Submitted by Dr. William G. Crumpton

My additional comments relate primarily to charge questions 3. 

Much of our panel’s discussion seemed to focus on issues related to connectivity and while connectivity is 

important, it is in many ways more important to consider 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 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 depressions from those downstream waters. Influence does 

not require a direct connection and “geographically isolated wetlands” 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 their areal extent (for example using the 

estimates of Miller et al., 2009 for Iowa). 

The apparent uncertainty over the connectivity of “geographically 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 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 related to cropped wetlands. Prior converted cropland 

and farmed wetlands are two distinct categories of wetland defined by the Food Security Act that have 

important implications with respect to both wetland protection and agricultural production. The 1985 Farm 

Bill established two categories of cropped wetlands, prior 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 treated as wetlands under the Swampbuster provisions 

of the 1985 Farm Bill. There are no USDA restrictions 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 protection 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 original drainage” could 

lose all USDA program benefits or face penalties. These 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 of the water that leaves agricultural watersheds. For 
William G. Crumpton, Ph.D. 

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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 unacceptable to ignore this issue in a report that 

addresses the connectivity and influence of wetlands on downstream waters. 
Kenneth W. Cummins, Ph.D. 

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Additional Comments Submitted by Dr. Kenneth W. Cummins 

Additional Comments (via email) 

There was a lot of discussion at the meeting about a reorganization of the information that was 

presented in the Document. I think the general thrust of the recommendation would improve the 

Document and not require much if anything in the way of new information. 

The organization would not be levels of connectivity but rather functional classes of connectivity: 

hydrologic, physical (geomorphic), chemical (nutrients/ 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. 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 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) wetlands 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 alterations...

10 223 ... lakes and lakes and reservoirs that form nodes in river systems. 

12 261-2 ...of sediment and organic matter... before they enter...

13 306-8 The impacts ... habitat, and ecology. The concept discussed 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 lakes 
Kenneth W. Cummins, Ph.D. 

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20 443 ... scientific community... not those ignoring non-peer reviewed 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 reviewed literature. 

21 477-8 Again, I would argue that this report has a more thorough and unbiased literature review 

than most “peer reviewed” papers. 

25 539 First Vannote et al., 1980 citation. Introduce River Continuum Concept phrase used 

therein. 

25 546 Fig. 3-2. You need a magnifying glass to distinguish ephemeral 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 or 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 add where warranted because it 

indicates at least a partial review of the subject is included; 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 distribution 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 Vannote 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 terrestrial (over land) movement and 

not by a hydrological pathway. 

54 1047-8 ...100 year floodplain. Introduce the concept of recurrence intervals (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 rule. 
Kenneth W. Cummins, Ph.D. 

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59 1139 The Metolius River emerges and immediately assumes the ecological characteristics of a 

fourth-order river, with no headwater biological inputs and constant year around flow and 

temperature that completely alters life history patterns 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 quick 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 figure. 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 classification of 

the drift: traits that influence invertebrate availability to salmonids. Can. J. Fish. Aquat. 

Sci. 54:1211-1234.] 

74 1363 ...movement and alter ecosystem function as in the case in which stream bank 

stabilization is accomplished by planting non-native willow to 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 represent 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 classification and not a blue line map 

criterion .If the tenets of connectivity in this report are 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 underestimation...), this raises 

important questions about the data. 

85 1604-06 Again, this might be a useful approximation, but it shows that, in general, map blue line 

analysis cannot be used to clarify the actual physical, chemical, and, especially 

biological, importance of geomorphic first-order channels in a watershed. 

85 1608 ...and river flows, as long as headwater streams are defined as second-order channels. 
Kenneth W. Cummins, Ph.D. 

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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 organic 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 measured 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 utilized by stream microbes and 

invertebrates. 

97 1858 ...diel changes typical of intermediate sized streams... and 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 diversity of these rivers. 

(Aquatic organisms have differing temperature optima, and a wide daily range of 

temperature excursion provides more species to spend at least 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 parts can 

dominate seasonally, e.g., catkins.) 

108 2106 Cite Petersen et al., 1989. [Petersen, R.C., K.W. Cummins, and G.M. Ward. 1989. 

Microbial and animal processing of detritus in a woodland stream. 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 invertebrates continue to feed 

and grow at 0 ̊C. In fact, the majority of shredders accomplish 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 acknowledged that connectivity can 

be on a diurnal scale as well as longer time periods. Weekly grab samples for DOC at 10 

locations throughout the Augusta Creek were taken in southwestern Michigan for two 
Kenneth W. Cummins, Ph.D. 

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years. Locations were sampled in sequence each week from 1 through 10 in the same 

sequential order. The data showed significant differences 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. 

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 that 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 example 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 freshwater 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 years that utilizes this functional 

categorization on a world- wide basis (e.g., Cushing 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 et al., 2008). The sequence 

is well known and has been demonstrated around the world (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 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 hyphomeycete biomass; 5) shredder 

feeding produces large amounts of FPOM (< 1 mm particle size feces and leaf 

fragments); 6) shredder feeding and temperature (number of degree days) accurately 
Kenneth W. Cummins, Ph.D. 

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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 riparian 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 (4th

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 likely density. 

146 2966-67 This is a basic tenet of the River Continuum Concept. 

147 2977 ...filterers (macroinvertebrates ...suspended FPOM)... Citation? See 146, 2970. 

148 3016-17 Again, it should be made clear that “richness” is taxa 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 width? 

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 temperatures 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 riparian 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. 

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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 streams 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 literature 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. Several more references could be put in related to this 

idea (Devito et al., 1999, Richardson et al., 2004, McCormick 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 downstream 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 sulphate 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) Nutrient additions by waterfowl to lakes and 

reservoirs: predicting their effects on productivity and water 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 wetland. 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., Bartsch, 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. 

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Malard, F., J.-L. Reygrobellet, J. Gibert, R. Chapuis, C. Drogue, T. Winiarsky and Y. Bouvet. (1994) 

Sensitivity of underground karst ecosystems to human perturbation - conceptual and methodological 

framework applied to the experimental site of Terrieu (Herault- 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. 

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Additional Comments Submitted by James W. La Baugh 

Post meeting comments 

In Reference to Charge Question Number 3, I offer the following text as one possible solution to the dilemma 

posed by use of the term non-riparian and channel origin wetlands. 

EPA connectivity panel - wetland classification note and suggestion 

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 wetlands, 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 classifications are not easily unified. In Winter and Woo 

(1990), a variety of lakes and wetlands were examined in the context of geologic settings, hydrologic 

processes controlling water balances, and physiographic settings. 

In the EPA connectivity draft, the need to define channel origin wetlands is not compelling. If channel origin 

wetlands were simply thought of in terms of being the headwaters 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 result 

would be two classes of wetlands, those associated directly 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 terms, riverine and non-riverine wetlands, also makes a 

distinction among wetlands: the first, those wetlands more likely to be directly connected by a surface water 

connection with a river, and second, those wetlands less likely 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 document. Such revision might solve the 

wetlands classification dilemma discussed on January 30, 2012 during the panel meeting. 

As an aside, Plate 2 from Winter and Woo (1990) is a nice portrayal of the fact that about half of North 

America is not humid. A figure for the lower 48 states derived 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 document. Conceptual framework material regarding 

connectivity and influence appearing in both the stream (section 4) and wetlands (section 5) sections could be 
James W. La Baugh, Ph.D. 

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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 ‘boxes’ 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 present 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 glossary:

The definition is correct. One of the other reviewers suggested 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 watershed 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 groundwater 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 regarding question 1. Figure 3-5 is inaccurate in its 

portrayal of local, intermediate, and regional flow systems. 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 divides 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 LaBaugh, 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 continental United States and Alaska and Hawaii:

Mention was made during the discussion that it might be useful to provide readers with the spatial context of 

ecoregions and hydrologic landscapes. Figure 8 on page S79 of Wollock 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 from the main focus of the conceptual framework 

because of the detail involved. 
James W. La Baugh, Ph.D. 

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INTERNAL DELIBERATIVE MATERIALS: DO NOT DISTRIBUTE, QUOTE, OR CITE

Comment about illustrating effects of pumping on groundwater flow 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) illustrations are provided herein. These are 

provided simply as examples of ways flow processes or connections have been illustrated in a variety of 

settings apart from the more general diagrams used from the Winter 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 freshwater wetlands in 

central Florida – A primer. U.S. Geological Survey Circular 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 Augmented 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 fluctuating 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. Geological 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 Islands—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; Pages 10 and 11 - various groundwater flow 

settings ] 

Faunt, C. C., editor, 2009, Groundwater availability of the Central 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 

INTERNAL DELIBERATIVE MATERIALS: DO NOT DISTRIBUTE, QUOTE, OR CITE

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, California. Chapter G in Stonestrom, D.A., Constantz, J., 

Ferré,T.P.A. and Leake, S.A., editors, 2007, Ground-Water Recharge 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 is provided below. 

http://pubs.usgs.gov/pp/pp1703/g/ pp1703g.pdf 

[Figure 4, page 163 – hydrologic features of intermittent streams in the Mojave Desert] 

Planert, M., and Williams, J.S., 1995, Ground Water Atlas 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 critical 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, Hartranft, Jeff, Cox, Scott, Scheid, Chris*, Potter, Noel*, 

Jenschke, Matthew*, Reed, Austin*, Matuszewski, Derek*, Kratz, 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 stream bank erosion: Reviews in Engineering 

Geology, special issue on “The Challenges of Dam Removal and 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., editors, 2009, Saltcedar and Russian Olive Control 

Demonstration Act Science Assessment. U.S. Geological Survey Scientific Investigations Report, 2009-5247, 

143 p. 

http://pubs.usgs.gov/sir/2009/5247/ 
James W. La Baugh, Ph.D. 

69 

INTERNAL DELIBERATIVE MATERIALS: DO NOT DISTRIBUTE, QUOTE, OR CITE

Document pertaining to analysis of changing hydrologic conditions in relation to potential 

for Devils Lake to spill to a river: 

Vecchia, A.V., 2008, Climate simulation and flood risk analysis 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 source of the information regarding the 

importance of moderate to highly permeable versus poorly permeable geologic substrates is Haitjema, H.M., 

1995. Analytic element modeling of groundwater flow. Academic Press, 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 State University Press, Ames, Iowa, p. 340-384. 

Gosselin, D.C., 1997, Major-ion chemistry of compositionally diverse lakes, Western Nebraska. U.S.A.: 

implications for paleoclimatic interpretations, Journal of Paleolimnology, 17:33-49. 

Document related to presence and characterization of playas: 

[Essential reference] Wood, W.W., 2002, Role of ground water 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 hydrological and biological interactions 

of prairie wetlands: 

Winter, T.C., ed., 2003, Hydrological, chemical, and biological 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 infiltration ponds to nearby lake: 

McCobb et al., 2003, Phosphorus in a Ground-Water Contaminant Plume Discharging 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/
James W. La Baugh, Ph.D. 

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INTERNAL DELIBERATIVE MATERIALS: DO NOT DISTRIBUTE, QUOTE, OR CITE

Document related to irrigation canal recharge of groundwater as source of baseflow in rivers 

inhabited by endangered fish species: 

Ely, D.M., 2003, Precipitation-Runoff Simulations of Current 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. 

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INTERNAL DELIBERATIVE MATERIALS: DO NOT DISTRIBUTE, QUOTE, OR CITE

Additional Comments Submitted by Dr. Mark C. Rains 

REVIEWER COMMENTS ON CONCEPTUAL FRAMEWORK: 

SUMMARY 

The key flaw in the document is that you arbitrarily break the landscape into three components, make the 

focus of the document on the individual discussions of those three components, and therefore make it difficult 

for you to show the inherent connectivity across these components. 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 rest of the document should be to support and 

better explain this conceptual framework. Then conceptual framework should start with the premise that all 

components of the landscape are connected, and that what differs is the degree to which they are connected 

and the importance of those connections to downstream systems. 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 should 

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 wetland or stream may be small. This, then, should 

the foundation to which you return throughout the document, always reminding the reader about how the 

supporting information in each of the three individual components relates to this conceptual model, and 

showing specifically how connections and their downstream effects are clear in some cases and not so much 

in others. 

DETAILED COMMENTS 

General Comment: Throughout the document, there were terminology 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 streams. These are often used interchangeably, even 

though they are not commonly used interchangeably, and are not defined 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 independently; 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 the case; rather, independent usage often seems to 

imply hydrological connectivity, and perhaps even surface-water 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 connectivity. 

General Comment: There are significant problems with some of 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 conceptual model, because it underlies the complex 
Mark C. Rains, Ph.D. 

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pathways and controls on hydrological connectivity. Lacking a proper conceptual framework in this regard, 

the document will fail to make a strong case not only for hydrological 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 differences in elevation (i.e., the downhill part of 

downgradient) and pressure. Pressure plays important roles in surface-water flows, but plays even more 

important roles in groundwater flows, including groundwater 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 wetland. 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 surface 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 generally include swamps, marshes, bogs, and similar 

areas.” This is very similar to a definition used later in the document (l. 3455-3456). What the authors refer to 

here is the Corps of Engineers Wetlands Delineation Manual (USACE 1987), which is guidance—which does 

not carry the full force of the law—on how to delineate a wetland and not a regulation—which does carry the 

full force of the law—on how a wetland is defined. One benefit of using the correct federal definition of a 

wetland found at 33 CFR 328.3(b)—which is more generic and inclusive, with rather vague boundaries—is 

that you won’t struggle so much in trying to explain what you 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 water in the saturated zone is under pressure and will 

rise up to the potentiometric surface if the confining layer is perforated (e.g., by a piezometer or even by a 

natural fracture, as occurs at many springs). See my comment titled “Figure 3-4”, below. 

l. 614-615: This is an inadequate definition of groundwater, because 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) groundwater and saturated-zone groundwater, respectively. 

l. 615-616: There are many saturated deposits that we do not commonly 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 has extremely low primary permeability, though it can 

have relatively high secondary permeability if there are abundant 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. 

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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 connected by unconfined aquifers, but many 

others are hydrologically connected by confined aquifers, especially 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, because they are so closely related. 

There are quite a few things wrong here, which stem from an 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 Toth (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 geologic heterogeneity. Still, you might decide to 

keep this, subject to some comments below, because there’s nothing 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, however, 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 larger in spatial scale and cross one or more 

groundwater divides (i.e., they cross under one or more potential local groundwater flows). This is not the 

case in Figure 3-5; the intermediate groundwater flow is from a local high to a local low (i.e., it’s another 

local groundwater flow) while the origin of the regional groundwater flow is a bit unclear. 

Regardless, I think that this is an incomplete conceptual model of flow from uplands to rivers and wetlands. 

There actually are four pathways that water can take from an upland to a river or wetland (Figure 1; Knighton 

1998). 

• Saturated Groundwater Flow (Pathway 1 in Figure 1): This is 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 through the unsaturated zone. This is commonly 

rapid flow through preferential flow paths, which can be soil cracks, animal burrows, or naturally formed 

soil pipes. 

• Infiltration-Excess Overland Flow, or Hortonian Overland Flow (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 thin layer of saturation blankets the surface, and excess 

rainfall runs off. 
Mark C. Rains, Ph.D. 

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• Saturated Overland Flow, or Dunne’s Mechanism of Overland Flow (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 conceptual model on which to base your reasoning. This is 

particularly true, because this emphasizes an important point, which I don’t think comes through in the 

document, which is that headwaters continue from the headwater stream up to the summit of the adjacent 

hillslope. Headwater streams and adjacent hillslopes are, in fact, integrally connected, to the extent that 

headwater streams cannot exist absent the adjacent hillslopes. This point is central to the argument made by 

Nadeau and Rains (2007), and can be seen (explicitly, in some cases) in the way that they discuss the 

references therein. (See, specifically, the way they discuss 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 that there is a separate item in the list that 

comprises “at the base of a mountain”, which could be either 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 above refers to this figure. 

l. 720-722: You might follow this with a specific example. For example, wetlands can be seasonally isolated, 

connected by groundwater flows, and connected by surface-water and groundwater flows (Rains et al., 2006, 

2008). 
Mark C. Rains, Ph.D. 

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l. 794-796: A good reference for the first three items in this 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 functions 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/organic 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” includes “alluvium” and “geologic materials”, but 

alluvium is a geologic material. I suggest omitting “geologic 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 this 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 for the recruitment of vegetation, especially willows and 

cottonwoods (McBride and Strahan 1984, Scott et al., 1996, Mahoney 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 the different the different hydrographs, which 

you try to do only in the context of climate, but are, in fact, 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 true, 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 precipitation 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, but 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. Because 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, because 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 definition. Similarly, all aquifers are permeable, so the 
Mark C. Rains, Ph.D. 

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term “permeable aquifer” is redundant. Also, permeability 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 not entirely correct. However, the general themes 

in the paragraph and in the figure are not entirely incorrect, 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 correct 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 sinkhole 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 secondary 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 extreme edge of the floodplain complex, and the 

effect is that riparian/floodplain wetlands do not connect strictly 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 historic channels are reoccupied on the historic 

floodplains, can decrease the duration of dry season baseflow 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 scientific 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 hydrologic regime of glacial terrain lakes. Journal 

of Hydrology 43:7–44. 

Bull, W.B. 1991. Geomorphic Response to Climate Change. Oxford University Press, New York. 

Childers, D.L., and J.G. Gosselink. 1990. Assessment of cumulative 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 American Society of Agricultural Engineers 

38:1719–1729. 
Mark C. Rains, Ph.D. 

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Dynesius, M., and C. Nilsson. 1994. Fragmentation and flow regulation of river systems in the northern third 

of the world. Science 266:753–762. 

Fleckenstein, J., M. Anderson, G. Fogg, and J. Mount. 2004. Managing surface water-groundwater to restore 

fall flows in the Cosumnes River. Journal of Water Resources Planning and Management 130:301–310. 

Freeman, M.C., C.M. Pringle, and C.R. Jackson. 2007. Hydrologic connectivity and the contribution of 

stream headwaters to ecological integrity at regional scales. 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 watershed, west-central Florida, 2003-2005 

and 2009. U.S. Geological Survey Scientific Investigations Report 2010–5092. U.S. Government 

Printing Office, Washington, DC. 

Haitjema, H.M., and S. Mitchell-Bruker. 2005. Are water tables a subdued replica of the topography? Ground 

Water 43:781–786. 

Hammersmark, C.T., M.C. Rains, and J.F. Mount. 2008. Quantifying the hydrologic effects of stream 

restoration in a montane meadow environment. River Research and 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 Agricultural Engineers 11:364–367. 

Hill, A.R. and D.J. Lymburner. 1998. Hyporheic zone chemistry and 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. Hyporheic 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 

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Mark C. Rains, Ph.D. 

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Meyer, L.D., S.M. Dabney, and W.C. Harmon. 1995. Sediment-trapping effectiveness of stiff-grass hedges. 

Transactions of the American Society of Agricultural Engineers 38:809–815. 

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Mark C. Rains, Ph.D. 

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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 there 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 would 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 “Connectivity...” 

in the report and all the workshop documentation led me to focus on the connections and not the effects. 

Given that the 1st, 2nd and 4th charge questions seem to be about consequences downstream, perhaps that 

should be better reflected in the title. It would certainly have drawn our attention more specifically to the

quantification of effects. 

As discussed in the meeting on the 30th January, the confusion over floodplain versus riparian needs to be 

clarified. Likewise, the category of non-floodplain wetlands needs more refinement as it covers an enormous 

range of wetland types. I think that if “floodplain” equals “riparian” in this scheme, then the use of floodplain 

should suffice. I found the use of “riparian” was not in line 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 intended 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. Perhaps 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 declarative statements, such as are included in the 

charge questions. The current 6 pages of chapter 6 seems insufficient compared to the enormous detail of the 

remainder of the document. 

Here are some additional references, from those that address spatially structured populations of amphibians in 

wetlands, to papers about effects from streams to estuaries, 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 riparian areas with water. 
John S. Richardson, Ph.D. 

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Additional references

Cole J. J., Y.T. Prairie, N. F. Caraco, W. H. McDowell, 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. Watershed effects on chemical properties of sediment 

and primary consumption in estuarine tidal flats: importance 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 British Columbia, Canada. Canadian Journal of 

Fisheries and Aquatic Sciences 65:38-46. 

Naiman, R.J., R.E. Bilby and P. Bisson. 2000. Riparian ecology and management in the Pacific coastal rain 

forest. BioScience. 50:996-1011. 

Werner E.E. et al., 2007. Turnover in an amphibian metacommunity: 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 status of amphibians. Ecology 77:2091-2097 

 DOI: 10.2307/2265703 
Joel W. Snodgrass, Ph.D. 

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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 floodplain wetlands and depend on overbank 

flows to connect floodplain wetlands for dispersal. 

Line 826: delete “has”—should be “This water can alter geomorphology...” 

Line 900: replace colon with period. 

Line 998: add “is”—should be “...the entire river system is difficult.” 

Lines 1445-1453: this paragraph describes a study, but does not report 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 fraction 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 streams 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 influences of beaver dams and failures of beaver 

dams. Geomorphology 71:48-60. 

Brooks, R. T., and E. A. Colburn. 2011. Extent and channel morphology of unmapped headwater stream 

segments of the Quabbin Watershed, Massachusetts. Journal of the American Water Resources 

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Fend, S.V., and R.O. Brinkhurst. 2000. New species of Rhynchelmis (Clitellata, Lumbriculidae), with 

observations on the Nearctic species. Hydrobiologia 428:1-59. 
Joel W. Snodgrass, Ph.D. 

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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. Alteration of North American streams by beaver. 

BioScience 38:753-762. 

Naiman, R. J., G. Pinay, C. A. Johnston, and J. Pastor. 1994. Beaver influences on the long-term 

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influence on fishes. American Fisheries Society Symposium 37:213-233. 

Roy, V., M. Amyot, and R. Carignan. 2009. Beaver ponds increase methylmercury concentrations in Canadian 

Shield streams along vegetation and pond-age gradients. Environmental Science & Technology 

43:5605–5611. 

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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., and 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 beavers 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 is better: beaver ponds on boreal streams as 

breeding habitat for the wood frog. Journal of Wildlife Management 70:1360–1371. 

Walsh, C. J., A. H. Roy, J. W. Feminella, P. D. Cottingham, P. M. Groffman, & R. P. Morgan. 2005. The 

urban stream syndrome: current knowledge and the search for a cure. 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 Systematics 27:337-363. 

Wiggins, G. B., R. J. MacKay, and I. M. Smith. 1980. Evolutionary and ecological strategies of animals in 

annual temporary pools. Archives fur Hydrobiologia 58(supplement):97-206. 
Joel W. Snodgrass, Ph.D. 

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Post-Meeting Comments 

As a general comment concerning the conceptual model introduced at the beginning of the document I think it 

would be a good idea to introduce both dimensions of time 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 isolation 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 spiraling length if the concept is applied to the entire gradient). Because streams and 

wetlands are most spatially 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 logical extension of the review to include the arguments presented earlier on the 

impacts of impervious surfaces and agricultural land conversion discussed in my original comments. 

On a related note to the development of the conceptual view, some changes to table 3-1 would help with 

clarity. I do like the idea of not having a specific sequence 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 large rivers. The examples I would cite here are 

adventitious streams verse true headwater streams (See Osborn and Wiley’s work that you currently cite) and 

channel wetlands along stream corridors (see Webster et 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 water 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. 

As far as the question concerning terminology for “geographically 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 adjacent to a stream. The definition of floodplain wetlands 

would be those wetlands that occur on the floodplain 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 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 provides another example of the influence of connectivity 

of low-land rivers to headwater streams on community 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. 
Joel W. Snodgrass, Ph.D. 

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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.. Ecology. 81:815-25. 

Crowl TA, McDowell WH, Covich AP, Johnson SL. 2001. Freshwater 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 stream. Canadian Journal of Fisheries and Aquatic 

Sciences 58: 470–478. 

March JG, Pringle CM, Townsend MJ, Wilson AI. 2002. Effects of freshwater shrimp assemblages on benthic 

communities along an altitudinal gradient of a tropical island stream. Freshwater Biology 47: 377–390. 

Pringle CM. 1996. Atyid shrimps (Decapoda: Atyidae) influence the spatial heterogeneity of algal 

communities over different scales in tropical montane streams, Puerto Rico. Freshwater Biology 35: 

125–140. 

Pringle CM, Blake GA, Covich AP, Buzby KM, Finley A. 1993. Effects 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 shrimp (Decapoda: Atyidae) on the depositional 

environment in a tropical stream: use of electricity for experimental 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 differences in organic matter. Ecology 80: 1860–1872. 

Riera JL, Magnuson JJ, Kratz TK, Webster KE. 2000. A geomorphic 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 within 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 Wisconsin, USA. Limnol. Oceanogr. 

41:977-984. 
Arnold van der Valk, Ph.D. 

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Additional Comments Submitted by Dr. Arnold van der Valk 

Some Additional Comments 

The main purpose of this report is to demonstrate the connectivity between streams and wetlands and 

navigable rivers. There are a large number of papers that have been published in the landscape ecology 

literature on connectivity and how to measure it. This literature is largely ignored in this report. A review of 

what is meant by connectivity and the various relevant ways 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 easier are to demonstrate than biological linkages. 

Not surprisingly the report emphasizes hydrological connectivity. 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 floodplains. 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 Mississippi 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 wetlands in the same class as wetlands that are the 

headwaters for streams (channel origin wetlands) is unidirectional surface flow (P. 42, ll. 813-815). Although 

some isolated wetlands like prairie potholes during high water events do have temporary surface connections 

to each other and even to nearby streams, many do not as noted. Many headwater wetlands, however, can 

have water backing up into them from streams during flooding events. It would be simpler to eliminate the 

use of the NRCW class from the report. The problem with lumping 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 wetlands. 

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 lacustrine). As defined by Cowardin et al. (1979), “The term 

SYSTEM refers here to a complex of wetlands and deepwater habitats that share the influence of similar 

hydrologic, geomorphologic, chemical, or biological factors.” Cowardin et al., recognize that intermittent 

streams are connected to perennial reaches of streams. They 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 
Arnold van der Valk, Ph.D. 

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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 clearly 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 wetlands 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 the National Wetland Inventory. Discussing the 

connectivity of palustrine wetlands to rivers would make it immediately 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 function. 

What is the relative importance of hydrological vs. biological connectivity? It is possible for some types of 

wetlands to have no surface water connection to streams. Given that all wetlands have hydric plants and a 

host of aquatic animals (invertebrates, birds, mammals, microorganisms, 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 connectivity and what minimum criterion or 

threshold is required to demonstrate biological connectivity. Does demonstrating the one-time movement or 

dispersal of one species from a river or a stream to a hydrologically isolated wetland (or vice versa) mean that 

the “isolated” wetland is not really isolated? If just establishing 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 rivers, a landscape approach is needed. One 

possible way to examine these linkages would be to use an HGM 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 this general approach. The more linkages that 

can be demonstrated the greater the influence of isolated wetlands in a watershed (or other comparable 

landscape unit) on the rivers in it. 

In summary, the authors of the report focus primarily on surface water flows as the major link between rivers 

and streams and wetlands. This primarily unidirectional flow 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 influence on navigable waters has rarely been 

documented. Whether such movements are essential for the persistence 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 consequence, in any landscape all bodies of water are 

interconnected and influence each other, but these interactions are often sporadic and asymmetrical. 
Mark S. Wipfli, Ph.D. 

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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 marine-derived nutrients, and their effects on 

headwater productivity in places that receive runs of anadromous fishes. It was suggested that a discussion of 

this topic be included in the report, and I agree that it should be included. This phenomenon is demonstrated 

through runs of adult Pacific salmon throughout the west coast 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 the 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 streams, at multiple trophic levels (periphyton, aquatic 

invertebrates, and fishes). The increased production in headwaters 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 into watersheds. In turn a portion of this 

invertebrate production can subsequently get delivered downstream from headwaters. 

Here are some of my papers on this topic. They in turn contain 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 inorganic fertilizer pellets: A test on multiple 

trophic levels in streamside experimental channels. Transactions of the American Fisheries Society 

139: 824-839. 

Heintz, R.A., M.S. Wipfli, and J.P. Hudson. 2010. Identification 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 salmon rearing in beaver ponds on 

the Copper River Delta, Alaska. Canadian Journal of Fisheries 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, southcentral 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 class 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. Chaloner. 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. 

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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 southeastern 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., Cederholm, C. J ., and W. J . Scarlett. 2001. Preliminary 

evaluation of the use of nitrogen stable isotope ratios to establish escapement levels for Pacific salmon. 

Fisheries 26:6-14. 

Claeson, S. M., J. L. Li, J. E. Compton, and P. A. Bisson. 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 salmon as vectors for the transfer of energy and 

nutrients between freshwater and marine environments. Freshwater Biology 48:21-27.

Nislow, K.H., and B.E. Kynard. 2009. The role of anadromous 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. Ringler, and J. G. Kennen. 1992. Factors limiting primary 

productivity in Lake Ontario tributaries receiving salmon migrations. 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 another avenue thorough which headwater streams 

are connected to downstream waters. Below are a few references for the report that discuss terrestrial 

invertebrate subsidies to streams, which in turn contain further references the authors of the EPA report can 

decide on their inclusion. 

Allan, J. D., M. S. Wipfli, J. P. Caouette, A. Prussian, 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. Chapman. 2007. Invading rainbow trout usurp a 

terrestrial prey subsidy to native char and alter their behavior, growth, and abundance. Oecologia 

153:461-470. 

Baxter, C. V., K. D. Fausch, and W. C. Saunders. 2005. Tangled webs: reciprocal flows of invertebrate prey 

link streams and riparian zones. Freshwater Biology 50(2):201- 220.
Mark S. Wipfli, Ph.D. 

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Kawaguchi, Y., and S. Nakano. 2001. Contribution of terrestrial invertebrates to the annual resource budget 

for salmonids in forest and grassland reaches of a headwater stream. Freshwater Biology 46:303-316. 

Kawaguchi, Y., S. Nakano, and Y. Taniguchi. 2003. Terrestrial 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 terrestrial invertebrates from tree canopies to a 

stream. Freshwater Biology 12:305-311. 

Nakano, S., H. Miyasaka, and N. Kuhara. 1999. Terrestrial-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 management increases terrestrial invertebrate 

inputs that feed trout in Wyoming rangeland streams. Transactions of the American Fisheries Society 

136:1216-1230.

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Appendix A: Individual Reviewer Comments 

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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/Professor 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 ecosystems in western North America. 

He also has active projects in the Andes of Peru and Bolivia, and in Slovakia and Poland in Europe. The 

main themes of his research are the role of hydrologic processes 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 restoration 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, private corporations, local governments, and nonprofit agencies. In the past ten years he has published 50 articles in peer reviewed journals, with most 

appearing in Ecological Applications, Journal of Hydrology, Canadian 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 Ecology, Hydrogeology Journal, Oecologia, 

Environmental Management, Wetlands, Water Resources Research, Hydrological Processes, Ecosystems, 

Plant and Soil, Journal of Range Management, Journal of Ecology, and Soil Biology and Biogeochemistry. 

David J. Cooper, Ph.D. 

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Peer Review Meeting of EPA’s Draft Report: Connectivity of Streams and Wetlands 

to Downstream Waters – A Review and Synthesis of the Scientific Evidence 

Comments submitted by Dr. David J. Cooper 

Overall Comments 

The authors of the report have done an excellent job of bringing 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 review indicates that our knowledge of hydrologic 

connections 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 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 each section of the report must have a discussion of 

what is unknown or uncertainties about connections, functions, and what future research is needed to support 

our understand of these processes. The report gives the impression that we know most of what is needed to 

understand and regulate these tributaries and wetlands. I think this is only partially correct. 

The temporal aspect of these jurisdictional identifications 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 is 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 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 noncontinuous 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 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 Evaluation 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 critical for inclusion because any 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 situated waters” as a way of extending our 

understanding beyond single sites. However, the geomorphic context of such 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 improvement. For example wetlands, riparian, floodplain, 

non-riparian wetland, etc. are all in 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 used as 
David J. Cooper, Ph.D. 

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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 areas 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 Pedro river is not a representative stream. Much 

attention has been paid to the San Pedro, making 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 

most has well developed riparian forests. In contrast most 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 and 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, and functions that effect downstream 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 within could also provide a good framework for discussing issues related to 

connectivity, and uncertainty in connections and ecological functions. Another potential is to organize around 

HGM wetland types, such as depression, slope, etc. although there is great variance through the U.S. on how 

basin/depression wetland function. 

Beavers are a key part of the biotic/hydrologic connection for 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 important 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 the 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. 

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Figure 3-6, all of these panels show a river connected via ground water 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 showing 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 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 and functioning of downstream waters. 

a) Are these conclusions 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. 

c) Was the reviewed literature cited and summarized correctly? 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 connected with the river network, and that 

their functions exert a strong influence on the character and functioning of downstream waters. 

a) Are these conclusions 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. 

c) Was the reviewed literature cited and summarized correctly? 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. 

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3. This report concludes that for non-riparian/non-floodplain wetlands that are not connected to the 

river network through a stream channel (i.e., geographically 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 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-reviewed 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 correctly? 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 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 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 evidence? 

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 correctly? If not please indicate where 

correction or revision is needed. 

The contribution of streams and wetlands on downstream waters is well known for flood water retention 

(the studies by Novitski 1978 in Wisconsin should be added). Denitrification 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 functions and values: the status of our 

understanding. Proc. National Symposium on Wetlands. Am Water Res Assoc, Minneapolis MN. 

Thomas C. Winter, Judson W. Harvey, O. Lehn Franke, William M. Alley. 2008. Surface and Ground water, 

a single Resource. USGS Circular 1139. 
David J. Cooper, Ph.D. 

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Hauer, F. R., B. J. Cook, M. C. Gilbert, E. C. Clairain, Jr., and R. D. Smith. 2001. The Hydrogeomorphic 

Approach to Functional Assessment: A Regional Guidebook for Assessing the Functions of Riverine 

Floodplain Wetlands in the Northern Rocky Mountains. Special Publ. WES, USCOE, Vicksburg, MS. 

p.255. 

Hauer, F. R., B. J. Cook, M. C. Gilbert, E. C. Clairain, Jr., and R. D. Smith. 2000. A regional guidebook: 

Assessing the functions of intermontane prairie pothole wetlands in the northern Rocky Mountains. 

Special Publ. WES, USCOE, Vicksburg, MS. p.189. 

THREE papers (PDFs attached) that you might consider referencing as they present original data on 

hydrologic connectivity on ephemeral and intermittent streams to riparian and wetland ecosystems 

Shaw, J. and D. J. Cooper. 2008. Watershed and stream reach 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. Stream/aquifer interactions at Great Sand Dunes 

National Monument, Colorado: Influences on interdunal wetland disappearance. Journal of Hydrology

271:77-100. 

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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 Department of Ecology, Evolution and Organismal 

Biology at Iowa State University, and Chair of ISU’s Environmental Science and Environmental Studies 

programs. He obtained his B.S. (interdisciplinary science) and M.S. (marine science) from the University of 

West Florida, his Ph.D. (limnology) from Michigan State University, 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 and effects of agricultural contaminants in wetlands, 

and the role of restored and constructed wetlands in watershed 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 performance 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 loads from tile-drained agricultural watersheds. 

William G. Crumpton, Ph.D. 

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Peer Review Meeting of EPA’s Draft Report: Connectivity of Streams and Wetlands 

to Downstream Waters – A Review and Synthesis of the Scientific Evidence 

Comments submitted by Dr. William G. Crumpton 

POST MEETING ADDITIONAL COMMENTS 

My additional comments relate primarily to charge question 3. 

Much of our panel’s discussion seemed to focus on issues related to connectivity and while connectivity is 

important, it is in many ways more important to consider 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 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 depressions from those downstream waters. 

Influence does not require a direct connection and “geographically isolated wetlands” 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 their areal extent (for example 

using the estimates of Miller et al., 2009 for Iowa). 

The apparent uncertainty over the connectivity of “geographically 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 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 related to cropped wetlands. Prior converted cropland 

and farmed wetlands are two distinct categories of wetland defined by the Food Security Act that have 

important implications with respect to both wetland protection and agricultural production. The 1985 Farm 

Bill established two categories of cropped wetlands, prior 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 treated as wetlands under the Swampbuster 

provisions of the 1985 Farm Bill. There are no USDA restrictions 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 protection 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 original 
William G. Crumpton, Ph.D. 

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drainage” could lose all USDA program benefits or face penalties. These 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 of 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 unacceptable to ignore this issue in a report that 

addresses the connectivity and influence of wetlands on downstream waters. 

RESPONSE TO 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 connections, individually or 

cumulatively, exert a strong influence on the character and functioning of downstream waters. 

a) Are these conclusions 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. 

c) Was the reviewed literature cited and summarized correctly? If not please indicate where 

correction or revision is needed. 

The conclusion that all streams are physically and chemically 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 streams 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 excluding 

certain channel origin wetlands that feed losing streams. The exception of certain wetlands spilling to 

losing streams as potentially not being connected to downstream 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 lack a connection to downstream waters, the 

conclusion that at least collectively streams exert a strong influence on the character and function of 

downstream waters is well supported. The report illustrates this through estimates of the fractions of 

river flow and material loads (nutrients, carbon, etc.) that originate in streams. 
William G. Crumpton, Ph.D. 

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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 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 appropriately. The report does a particularly good 

job in summarizing the complex nature of stream 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. 

2. This report concludes that open water and wetlands in riparian areas and floodplains of streams 

and rivers are physically, chemically, and biologically connected with the river network, and that 

their functions exert a strong influence on the character and functioning of downstream waters. 

a) Are these conclusions 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. 

c) Was the reviewed literature cited and summarized correctly? If not please indicate where 

correction or revision is needed. 

The conclusion that wetlands in riparian areas and floodplains 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 riparian areas and floodplains of certain 

permanently losing steams that are never connected to downstream 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 migration of organisms. 

The conclusion that wetlands in riparian areas and floodplains of streams and rivers exert a strong 

influence on the character and function of downstream waters is well supported by the scientific 

evidence – at least for the systems collectively, and that 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 the 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 reasonably concluded. 
William G. Crumpton, Ph.D. 

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3. This report concludes that for non-riparian/non-floodplain wetlands that are not connected to the 

river network through a stream channel (i.e., geographically 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 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-reviewed 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 correctly? If not please indicate where 

correction or revision is needed. 

The conclusion that in the case of non-riparian/non-floodplain wetlands that are not connected to the 

river network through a stream channel, connectivity and isolation varies within a watershed and over 

time is well supported by the scientific evidence. 

The conclusion that the literature reviewed does not provide sufficient 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 downstream waters. The report should attempt to provide guidance on how to distinguish these two 

categories (perhaps using soils and other indicators). The report 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 introduced on lines 52-54 on page 3 of the 

Introduction and repeated throughout the report. It is well illustrated 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 isolated wetlands since swales can be “upland”. However, it would also include in this 

category prairie pothole depressions that spill over onto wetland flats or slope wetlands rather than to a 

channel. Wetland depressions that spill over to wetland systems (including wetland 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 truly geographically isolated. 

The report provides reasonable coverage of the relevant peer-reviewed literature on connection and 

isolation of non-riparian/non-floodplain wetlands to the downstream waters but does fall short in a few 

areas. 
William G. Crumpton, Ph.D. 

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The report fails to adequately address the effect of subsurface 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 example lines 5166-5170 on pages 249-

250 of section 5.8.3.1). The report states that “When potholes are artificially connected to streams 

and lakes though drainage, isolation is eliminated and they 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 is given to the importance of subsurface 

“tile” drainage which is ubiquitous throughout the Corn Belt and many other areas. The report 

mentions only briefly that “drains fitted at the bottom of potholes connected to shallow subsurface 

pipes often discharge to 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 to downstream waters. 

Specifically, do surface intakes of subsurface drainage pipes (“tile drains”) provide a direct 

connection to downstream waters for what might otherwise be considered geographically isolated 

wetlands? 

The report in part uses HGM (hydrogeomorphic) wetland classification and could benefit from a 

review of the wetland classes in this system. Important 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 these landscapes. 

The report should also provide information on the relationship 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 isolated 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 surface outflow and connectivity is expected in 

wetter portions of the prairie pothole but extends 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). 
William G. Crumpton, Ph.D. 

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A broader analysis of this pattern for the Prairie Pothole is provided by Johnson et al. (2005.

Vulnerability of northern prairie wetlands to climate change. Bioscience 55: 863-873). Their 

models of wetland water regimes suggest that spillover to downstream waters is a common 

occurrence in the wetter portions 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 flow 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 between the more interconnected wetlands of the Des Moines Lobe 

and the more isolated wetlands of the drier portions of the Prairie Pothole Region. 

The literature is for the most part cited and summarized correctly. However, in several places (line 1435-

1468 and others), the report incorrectly describes the subregions of the Prairie Pothole Region, 

essentially ignoring the Des Moines lobe. This is the 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. 

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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 evidence? 

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 correctly? 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 common 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 in the treatments of streams, riparian/floodplain 

wetlands, and non-riparian/non-floodplain wetlands. 

The literature relevant to this topic was cited and summarized appropriately although its dispersion 

throughout the document makes it less easily accessible than that of the other topics. 

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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 Cooperative Fisheries Research Unit - both at Humboldt State 

University. 

Over the past 40 years, Dr. Cummins has been involved in research 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 Scientist at the South Florida Water Management 

District in the Everglades Restoration Program. 

“The River Continuum Concept” (RCC), which he co-authored, relates the physical template 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- floodplain interactions, localized tributary 

effects on larger rivers, discontinuities in the RCC imposed 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 genera 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 invertebrate 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.; Hydrobiologia; Arch. Hydrobiol.; Freshwat. Biol.; 

Freshwat. Invert.; Oikos; Annals Limnol.; Invert. Biol.; Amer. 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. 

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Peer Review Meeting of EPA’s Draft Report: Connectivity of Streams and Wetlands 

to Downstream Waters – A Review and Synthesis of the Scientific Evidence 

Comments submitted by Dr. Kenneth W. Cummins

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 and functioning of downstream waters. 

a) Are these conclusions supported by the scientific evidence? 

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 loops, the 

unidirectional flow of streams creates open cycles 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 hydrology 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 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 suggested using air-shed, 

watershed, and ground-watershed to categorize all the approximately definable inputs 

and cycles with in a region. 

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

alternatives to this statement should be acknowledged. For example, 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 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 in most headwater streams. 
Kenneth W. Cummins, Ph.D. 

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 Here, and elsewhere, the point should be driven home that stream order is a 

geomorphic concept and probably never should be inferred from blue 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., California Forest Practices Rules, Section 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 spawning. 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. Class 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 access roads) “and are 

capable of sediment transport to Class I and II waters under normal high water flow 

conditions. (Cummins, K.W. and M.A. Wilzbach. 2005. The inadequacy of the fishbearing criterion for stream management. Aquatic Sciences. On line; 

http://www.birkhauser.ch, pp 1-6). 

24 531 ...symmetry ratio... another way is link number, which sums the total number of 

first-order tributaries entering a watershed of a given order. Fig. 3-1 shows no firstorder tributaries entering directly into the third-order mainstem which would be quite 

unusual. Link number is a useful measurer for stream ecologists working at the 

watershed scale because 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 indication 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 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, fisheries managers, and 

forestry managers all have different concepts (or biases) about the definition of the 

width. For example, stream ecologists may focus on the width necessary to provide 

the width that supplies plant litter that constitutes the primary energy source of 

headwater stream ecosystems, fisheries managers are concerned with the width 

necessary to insure the input of large wood which is the mainstay 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 defining 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 with a dashed line at the ends. 

The figure caption should explain that the dash lines indicate that the boundary of the 

riparian zone depends upon the function being considered (e.g., Gregory et al., 1991). 
Kenneth W. Cummins, Ph.D. 

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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 bacteria. This significantly 

delays the export of organic matter down river. DOM almost universally accounts for 

50% of all the organic matter in transport in all order streams (Vannote et al., 1980 

and the Minshall et al., River Continuum publications). This retention of FPOM, 

rather than loss as DOM, has major consequences for stream and river invertebrates 

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 intervals involve flows too small 

to cause significant changes in stream channel geomorphology, and very long 

recurrence intervals cause very major alterations in channel 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 forest landscapes. Pp. 91-138 

in: Salo, E. O. and T. W. Cundy. (eds.). Streamside management: forestry and 

fisheries interactions. Institute of Forest Resources, Univ. Washington, 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 America, Central and south 

America, Europe, Africa, Asia, Australia and New Zealand, 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 editors presents an overview of 

stream ecosystems. The River Continuum Conceptual Model (Vannote et al., 1980) is 

reproduced in the Introduction. This is the model that relates stream/river ecological 

structure and function to the position along the downstream trajectory. (Cushing, C. 

E., K. W. Cummins, and G. W. Minshall. 2006. River and stream 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 et al. (1989) 

and not to the 1000 m cited in this report. 

112 2197 ...snow melt. Approximately 50% of transported carbon was DOC 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 anaerobic storage of CPOM, e.g., 

leaf litter, greatly delays breakdown of CPOM to FPOM in 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. 

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DC Mahan, and R.L. Mattingly. 1980. Processing of confined and naturally entrained 

leaf litter in a woodland stream ecosystem. Limnol. Oceanogr. 25:952-957.] 

120 2382 Wilzbach and Cummins (1989 ) demonstrated a higher % mortality among drifting 

individuals than their benthic counterparts. This raises the 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 the contribution being to 

the downstream detrital suspended load. (Wilzbach, M. A. and K. W. Cummins. 

1989. An assessment of short-term depletion of stream macrobenthos 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. 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 majority of introduced 

leaf litter in a forested second-order stream by reported to be about 100 m by 

Cummins et al. (1989). [Travel distance of leaf litter was reported from the time the 

litter is wetted. Senescent Ginkgo leaves were used in these 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 the native riparian tree 

species in eastern headwater streams.] 

Attached is a figure that might be of interest to some people at the meeting. I make no suggestion 

whatsoever that this Figure should be any part of the report. It is merely a “snap shot” offered in support 

of the argument that I did make in the report about including 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 first- to third-order). The photograph is not 

unique; this sort of 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, Oregon, New Mexico, Yellowstone Park (Wyoming 

and Montana), Idaho, Michigan, Pennsylvania, Maryland, Florida, Sweden, Denmark, Italy, Australia, 

New Zealand, Brazil, and Guinea West Africa. 
Kenneth W. Cummins, Ph.D. 

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Fig. A. Conditioned red alder leaf eaten by caddisfly (Trichoptera) larvae. Note: better conditioned (higher 

aquatic hyphomycete fungal biomass) soft tissues eaten in preference to the poorly conditioned midrib and 

major 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 Technical 

Charge Question 1. 

So, as I argued in one of my comments in Response to Charge question 1, this world wide and highly 

predictable connection between riparian vegetation and 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. 

c) Was the reviewed literature cited and summarized correctly? If not please indicate where 

correction or revision is needed. 

The Literature that was cited was summarized correctly. 

2. This report concludes that open water and wetlands and riparian areas and floodplains of streams 

and rivers are physically, chemically, and biologically connected with the river net work, and that 

their functions exert a strong influence on the character and functioning of downstream waters. 

a) Are these conclusions supported by the scientific evidence? 

The conclusions are supported by the scientific evidence. 
Kenneth W. Cummins, Ph.D. 

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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 headwater streams are not the 

initial source of river networks should be flagged. For example, the Yellowstone 

River (one of the longest and largest un-dammed rivers 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-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 26, 559, there is little 

agreement about this, because the width is dependent upon the function being 

considered or the management objectives dependent upon the width as define by 

regulations. For example, foresters interested in timber harvest will argue for the 

smallest width possible while fisheries managers will argue 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 against the potential disruptive 

effects on the aquatic ecosystem involved, e.g., stream or wetland. A very important 

point about connectivity between the riparian zone and the adjacent aquatic system 

and, therefore, the connectivity downstream is that the plant species composition of 

the riparian 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). This 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. The 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. 

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c) Was the reviewed literature cited and summarized correctly? 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-floodplain wetlands that are not connected to the 

river network through a stream channel (i.e., geographically 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 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 evidence? 

The conclusions are supported by the scientific evidence. 

In general they are supported by the literature cited. However, 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 about a reorganization of the information that 

was presented in the Document. I think the general thrust of the recommendation would improve the 

Document and not require much, if anything, in the way of new information. 

The organization would not be levels of connectivity but rather functional classes of connectivity: 

hydrologic, physical (geomorphic), chemical (nutrients/ 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 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 streams and wetlands of various types are, the lower 

probability they will exhibit high connectivity on any time scale. 

This more functional approach would provide, I believe, a better 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 biological isolation, because migrations 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 literature on those topics, including evidence of 

connectivity and isolation as presented. However, if a different organization of the report is adopted, as 

discussed above, a reorganization of the references cited would be 
Kenneth W. Cummins, Ph.D. 

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c) Was the reviewed literature cited and summarized correctly? 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 evidence? 

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 literature 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 transfer 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, respectively. 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 or both of these appear in essentially every subsection of the entire report. In reading the report I concluded 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 correctly? If not please indicate where 

correction or revision is needed. 

The reviewed literature was cited and summarized correctly, or relevant comments were covered under 

the first three Charge Questions (e.g., comments about adaptations by invertebrate life cycles to 

accommodate periodic drying, in which the annual predictable seasonal flows of intermittent streams 

have more taxa adapted to the condition than in ephemeral streams, 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 reorganization of the information that was 

presented in the Document. I think the general thrust of the recommendation would improve the 

Document and not require much if anything in the way of new information. 

The organization would not be levels of connectivity but rather functional classes of connectivity: 

hydrologic, physical (geomorphic), chemical (nutrients/ pollutants), and biological (ecological). 

Within each of these classes there would be continua of connectivity described as probabilities. 
Kenneth W. Cummins, Ph.D. 

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Namely spatial and temporal probabilities of degree of connectedness. 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 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) wetlands 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 alterations...

10 223 ... lakes and lakes and reservoirs that form nodes in river systems. 

12 261-2 ...of sediment and organic matter... before they enter...

13 306-8 The impacts ... habitat, and ecology. The concept discussed 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 lakes 

20 443 ... scientific community... not those ignoring non-peer reviewed 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 reviewed literature. 

21 477-8 Again, I would argue that this report has a more thorough and unbiased literature 

review than most “peer reviewed” papers. 

25 539 First Vannote et al., 1980 citation. Introduce River Continuum Concept phrase used 

therein. 

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

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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 or 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 add where warranted because it 

indicates at least a partial review of the subject is included; 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 distribution 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 Vannote 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 terrestrial (over land) movement and 

not by a hydrological pathway. 

54 1047-8 ...100 year floodplain. Introduce the concept of recurrence intervals (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 rule. 

59 1139 The Metolius River emerges and immediately assumes the ecological characteristics of 

a fourth-order river, with no headwater biological inputs and constant year around flow 

and temperature that completely alters life history patterns 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 quick flow for “paved” urban 

stream watersheds. 
Kenneth W. Cummins, Ph.D. 

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65 1240-42 See comment for 11, 253-60. 

66. 162 Fig. 3-19. The use of link number can be seen in the figure. 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 classification 

of the drift: traits that influence invertebrate availability to salmonids. Can. J. Fish. 

Aquat. Sci. 54:1211-1234.] 

74 1363 ...movement and alter ecosystem function as in the case in which stream bank 

stabilization is accomplished by planting non-native willow to 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 represent 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 classification and not a blue line map 

criterion. If the tenets of connectivity in this report are 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 underestimation...), this raises 

important questions about the data. 

85 1604-06 Again, this might be a useful approximation, but it shows that, in general, map blue line 

analysis cannot be used to clarify the actual physical, chemical, and, especially 

biological, importance of geomorphic first-order channels in a watershed. 

85 1608 ...and river flows, as long as headwater streams are defined 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 organic 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. 

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94 1796 LWD in stream of the western Cascades in Oregon measured 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 utilized by stream microbes 

and invertebrates. 

97 1858 ...diel changes typical of intermediate sized streams... and 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 diversity of these rivers. 

(Aquatic organisms have differing temperature optima, and a wide daily range of 

temperature excursion provides more species to spend at least 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 parts can 

dominate seasonally, e.g., catkins. 

108 2106 Cite Petersen et al., 1989. [Petersen, R.C., K.W. Cummins, and G.M. Ward. 1989. 

Microbial and animal processing of detritus in a woodland stream. 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 invertebrates continue to feed 

and grow at 0 ̊C. In fact, the majority of shredders accomplish 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 acknowledged that connectivity can 

be on a diurnal scale as well as longer time periods. Weekly grab samples for DOC at 

10 locations throughout the Augusta Creek were taken in southwestern Michigan for 

two years. Locations were sampled in sequence each week from 1 through 10 in the 

same sequential order. The data showed significant differences 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. 

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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 that 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 example 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 freshwater 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 years that utilizes this 

functional categorization on a world- wide basis (e.g., Cushing 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 et al., 2008). The 

sequence is well known and has been demonstrated around the world (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 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 

hyphomeycete biomass; 5) shredder feeding produces large amounts of FPOM (< 1 mm 

particle size feces and leaf fragments); 6) shredder feeding and temperature (number of 

degree days) accurately 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 riparian 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 

(4th 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.] 
Kenneth W. Cummins, Ph.D. 

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146 2965 ...richness... Is this species richness? It would be more likely density. 

146 2966-67 This is a basic tenet of the River Continuum Concept. 

147 2977 ...filterers (macroinvertebrates ...suspended FPOM)... Citation? See 146, 2970. 

148 3016-17 Again, it should be made clear that “richness” is taxa 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 width? 

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 temperatures 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 riparian corridors are dominated by 

shrubby or tree (red) alders that are nitrogen fixers and constitute a major source of 

nitrogen. 
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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 leading 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 rates 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 received more than $5 million in extramural funding 

from various agencies including the National Science Foundation, 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 Montana State University in 1988 and joined the KState Division of Biology faculty in 1990. He was hosted on sabbatical at the National Institute of Water and 

Atmospheric Research in Christchurch New Zealand in 1996. With over 125 refereed publications to his 

credit, Walter Dodds is the author of three books in his discipline. His textbook Freshwater Ecology: 

Concepts and Environmental Applications is one of the defining textbooks in the field. 

Walter K. Dodds, Ph.D. 

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Peer Review Meeting of EPA’s Draft Report: Connectivity of Streams and Wetlands 

to Downstream Waters – A Review and Synthesis of the Scientific 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 lag to identify key functions. This approach really 

allows the issue at hand to be very clearly explored. However, this framework is not really clearly delineated 

throughout the document, and I think the document would be strengthened 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 connectivity. 

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 and functioning of downstream waters. 

a) Are these conclusions supported by the scientific evidence? 

For the most part, these conclusions are supported by the scientific 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. 

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 is well referenced. There are so many references 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 correctly? If not please indicate where 

correction or revision is needed. 

Yes, the literature was reviewed and cited correctly. One minor addition could be that there is one 

reference that is cited, Dodds and Oakes 2006 that indicates 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 reaches as well, although figure 3-13 helps. 

Also a figure with a longitudinal cross 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 it 
Walter K. Dodds, Ph.D. 

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looks like everything flows into everything else through the river.. 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 figure 3-14 is somewhat misleading as it ignores 

cycling through inorganic forms. 

Line 1031, these streams flow during and immediately following precipitation. 

A clearer discussion of when increased connectivity can be bad (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 change longitudinal patterns, but much less 

severely and in very different ways from dams. 

Line 1793. In the Flint Hills of Kansas, wood does not accumulate in small streams, and such streams 

are an important source of large wood to downstream rivers. This wood is very important habitat as well 

as a geomorphologic force in rivers. This statement might need to be qualified a bit. 

Line 2495, might want to discuss the Falke and Gido 2006 (in references) work here on reservoirs 

disconnecting small streams from each other. 

Line 2560. This could be stated more strongly. The evidence unequivocally 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., 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 ecoregions, 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 establishing reference nutrient concentrations across watersheds 

affected by humans. Limnology and Oceanography Methods, 2, 333-341. 

Line 2750, these are still net heterotrophic, so they are derived 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 
Walter K. Dodds, Ph.D. 

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2. This report concludes that open water and wetlands in riparian areas and floodplains of streams 

and rivers are physically, chemically, and biologically connected with the river network, and that 

their functions exert a strong influence on the character 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-reviewed 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 cited. 

c) Was the reviewed literature cited and summarized correctly? 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 understand that the authors of this document did not 

want to leave out riparian 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 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) Flooding to restore connectivity of 

regulated, large-river wetlands. Bioscience, 48, 721-733. 

Galat, D.L. & Lopkin, R. (2000) Restoring ecological integrity 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 restoration 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. 

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3. This report concludes that for non-riparian/non-floodplain wetlands that are not connected to the 

river network through a stream channel (i.e., geographically 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 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 other waters, then the only output of water must be 

evaporation. If this is the case then 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 

connected to downstream waters either directly or through groundwater. 

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. 

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 connections in the Highland Lake District of 

Wisconsin, and these connections include wetlands. 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 productivity, Trout Lake watershed, northern Wisconsin, USA. Journal of Hydrology,

320, 370-384. 

There is a huge amount of work on hydrologic and chemical connection 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 inconsistent with the rest of the report. 

c) Was the reviewed literature cited and summarized correctly? 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 natural 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. 

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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 evidence? 

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 management 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-reviewed 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 correctly? 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 streams 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 literature 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. Several more references could be put in related to 

this idea (Devito et al., 1999, Richardson et al., 2004, McCormick 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 downstream 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. 

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Devito, K.J., Hill, A.R. & Dillon, P. (1999) Episodic sulphate 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) Nutrient additions by waterfowl to lakes and 

reservoirs: predicting their effects on productivity and water 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 wetland. 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., Bartsch, 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 perturbation - conceptual and methodological 

framework applied to the experimental site of Terrieu (Herault- 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.) 
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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 Survey, Reston, Virginia, March 1995 to 

present. Research efforts have been directed at the hydrological mechanisms controlling chemical fluxes 

between lakes and wetlands, their watersheds, and the atmosphere, including directly measured 

contributions by groundwater. This includes investigation of chemical 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, North Dakota, Minnesota, New Hampshire, and Guam. 

Study of the interaction of lakes and wetlands with groundwater has included examination of multiple lakes 

and wetlands within common groundwater flow systems at sites 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 (Limnology 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 publications 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. 

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Peer Review Meeting of EPA’s Draft Report: Connectivity of Streams and Wetlands to 

Downstream Waters – A Review and Synthesis of the Scientific Evidence 

Comments submitted by Dr. James W. La Baugh 

TECHNICAL CHARGE QUESTIONS: 

(Note: underlined text in my original responses to the charge questions identifies critical or essential 

suggestions) 

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 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 supports conclusion 1. The document, 

however, includes some conceptual inconsistencies 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 interaction with 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 representing 

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 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 alluvial 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 formation 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...” is 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. 

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An aquifer by definition is “A body of rock that contains sufficient saturated permeable material 

to conduct ground water and to yield economically significant 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.; or “An aquifer is a formation, group 

of formations, or part of a formation that contains sufficient 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 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 the key points 

being made about flow systems while being consistent with correct use of technical terms. It is not 

at all clear why the explanation includes reference to intermediate 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 from beyond 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 deleting vagility to simplify the text.

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. 

• A useful reference regarding the interaction of streams and groundwater is absent from the 

references – Jones, J.B., and Mulholland, P.J., eds. 2000. Streams and Ground Waters, Academic 

Press, 425 p. 

c) Was the reviewed literature cited and summarized correctly? 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 citation 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 connected with the river network, and that 

their functions exert a strong influence on the character 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 riparian wetlands to streams and rivers would benefit 

from clarification, as noted below. 
James. W. La Baugh, Ph.D. 

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• 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 would contribute to baseflow? 

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. 

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

c) Was the reviewed literature cited and summarized correctly? 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-floodplain wetlands that are not connected to the 

river network through a stream channel (i.e., geographically 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 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 overall synthesis of the cited literature provided in the 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 and hydrological isolation? The issue of 

connectivity would seem to be a function 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, 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. 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 geological 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 groundwater? What about the importance of 
James. W. La Baugh, Ph.D. 

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topographic setting with respect to the presence 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-riparian wetland with 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 particle 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-permeability 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 characteristic of prairie pothole 

wetlands is loss of sediment due to wind erosion during periods 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 prairie 

pothole wetlands and streams or river networks is the presence 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 streams 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 what 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 transporting 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 substrate is impermeable, by definition it will not 

contain a surficial aquifer. A low-permeable substrate could contain a shallow groundwater 

system separated from a deeper regional aquifer by a confining bed. 
James. W. La Baugh, Ph.D. 

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• Page 270, lines 5617 to 5623 – The content of the paragraph reinforces the need to provide 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-reviewed literature on these topics, including 

evidence of connectivity and isolation? If not please indicate which references are 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 flow in a variety of landscapes is 

Richardson, J.L., and Vepraskas, M.J., editors, 2001, Wetland soils: genesis, hydrology, 

landscapes, and classification. Lewis Publishers, Boca Raton, Florida, 417 p. 

• Page 283, lines 6053 to 6056 – Entry for the cited literature source is not complete 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 complete regarding 

the publication information. 

The correct entry for the Vining 2002 should be revised as follows – 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 follows 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 correctly? 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 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 wetlands was summarized correctly. 
James. W. La Baugh, Ph.D. 

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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 evidence? 

• In the section 6 of the document containing the set of conclusions (pages 266 to 271), the 

conclusion noted as 4 above was not presented. Nor was a fourth 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 problematic. 

b) Does the report include the most relevant peer-reviewed 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 correctly? 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 following text as one possible solution to the 

dilemma posed by use of the term non-riparian and channel origin wetlands. 

EPA connectivity panel - wetland classification note and suggestion 

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 wetlands, 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 classifications are not easily unified. In Winter and Woo 

(1990), a variety of lakes and wetlands were examined in the context of geologic settings, hydrologic 

processes controlling water balances, and physiographic settings. 

In the EPA connectivity draft, the need to define channel origin wetlands is not compelling. If channel origin 

wetlands were simply thought of in terms of being the headwaters 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 result 

would be two classes of wetlands, those associated directly 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 terms, riverine and non-riverine wetlands, also makes a 

distinction among wetlands: the first, those wetlands more likely to be directly connected by a surface water 
James. W. La Baugh, Ph.D. 

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 INTERNAL DELIBERATIVE MATERIALS: DO NOT DISTRIBUTE, QUOTE, OR CITE

connection with a river, and second, those wetlands less likely 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 document. Such revision might solve the 

wetlands classification dilemma discussed on January 30, 2012 during the panel meeting. 

As an aside, Plate 2 from Winter and Woo (1990) is a nice portrayal of the fact that about half of North 

America is not humid. A figure for the lower 48 states derived 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 document. Conceptual framework material regarding 

connectivity and influence appearing in both the stream (section 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 ‘boxes’ 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 present 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 glossary:

The definition is correct. One of the other reviewers suggested 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 watershed 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 groundwater 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 
James. W. La Baugh, Ph.D. 

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systems is introduced. As noted in my first comment regarding question 1. Figure 3-5 is inaccurate in its 

portrayal of local, intermediate, and regional flow systems. 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 divides 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 LaBaugh, 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 continental United States and Alaska and Hawaii:

Mention was made during the discussion that it might be useful to provide readers with the spatial context of 

ecoregions and hydrologic landscapes. Figure 8 on page S79 of Wollock 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 from the main focus of the conceptual framework 

because of the detail involved. 

Comment about illustrating effects of pumping on groundwater flow 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) illustrations are provided herein. These are 

provided simply as examples of ways flow processes or connections have been illustrated in a variety of 

settings apart from the more general diagrams used from the Winter 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 freshwater wetlands in 

central Florida – A primer. U.S. Geological Survey Circular 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 Augmented 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 fluctuating water level; Figure 11, page 24 – 

example of flow system in relation to wetland] 
James. W. La Baugh, Ph.D. 

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 INTERNAL DELIBERATIVE MATERIALS: DO NOT DISTRIBUTE, QUOTE, OR CITE

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. Geological 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 Islands—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; Pages 10 and 11 - various groundwater flow 

settings ] 

Faunt, C. C., editor, 2009, Groundwater availability of the Central 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 in the Western Mojave Desert, California. Chapter 

G in Stonestrom, D.A., Constantz, J., Ferré,T.P.A. and Leake, S.A., editors, 2007, Ground-Water Recharge 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 is provided below. 

http://pubs.usgs.gov/pp/pp1703/g/pp1703g.pdf 

[Figure 4, page 163 – hydrologic features of intermittent streams in the Mojave Desert] 

Planert, M., and Williams, J.S., 1995, Ground Water Atlas 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. 

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* Documents referred to in general discussion, but not critical 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 milldams

Merritts, Dorothy, Rahnis, Michael, Walter, Robert, Hartranft, Jeff, Cox, Scott, Scheid, Chris*, Potter, Noel*, 

Jenschke, Matthew*, Reed, Austin*, Matuszewski, Derek*, Kratz, 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 stream bank erosion: Reviews in Engineering 

Geology, special issue on “The Challenges of Dam Removal and 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., editors, 2009, Saltcedar and Russian Olive Control 

Demonstration Act Science Assessment. U.S. Geological Survey Scientific Investigations Report, 2009-5247, 

143 p. 

http://pubs.usgs.gov/sir/2009/5247/ 

Document pertaining to analysis of changing hydrologic conditions in relation to potential

for Devils Lake to spill to a river

Vecchia, A.V., 2008, Climate simulation and flood risk analysis 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 source of the information regarding the 

importance of moderate to highly permeable versus poorly permeable geologic substrates is Haitjema, H.M., 

1995. Analytic element modeling of groundwater flow. Academic Press, 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 State University Press, Ames, Iowa, p. 340-384. 
James. W. La Baugh, Ph.D. 

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 INTERNAL DELIBERATIVE MATERIALS: DO NOT DISTRIBUTE, QUOTE, OR CITE

Gosselin, D.C., 1997, Major-ion chemistry of compositionally diverse lakes, Western Nebraska. U.S.A.: 

implications for paleoclimatic interpretations, Journal of Paleolimnology, 17:33-49. 

Document related to presence and characterization of playas:

[Essential reference] Wood, W.W., 2002, Role of ground water 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 hydrological and biological interactions

of prairie wetlands

Winter, T.C., ed., 2003, Hydrological, chemical, and biological 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 infiltration ponds to nearby lake

McCobb et al., 2003, Phosphorus in a Ground-Water Contaminant Plume Discharging 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 groundwater as source of baseflow in rivers

inhabited by endangered fish species

Ely, D.M., 2003, Precipitation-Runoff Simulations of Current 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/ 

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Mark C. Rains, Ph.D. 

Associate Professor 

University of South Florida. 

Tampa, FL 

Mark Rains is an ecohydrologist with a B.A. in Ecology, Behavior, 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 sectors 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 landscape-scale hydrological connectivity, (b) the roles that 

hydrological processes play in governing ecosystem structure and 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, headwater streams and mainstem rivers, and 

mangroves and lagoons. Dr. Rains has additional service-related 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 science and policy in wetland regulatory programs, 

including past and ongoing work related to providing the scientific 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 and 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, national, and international meetings and university 

colloquia. 

Mark C. Rains, Ph.D. 

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Peer Review Meeting of EPA’s Draft Report: Connectivity of Streams and Wetlands to 

Downstream Waters – A Review and Synthesis of the Scientific Evidence 

Comments submitted by Dr. Mark C. Rains 

REVIEWER COMMENTS ON CONCEPTUAL FRAMEWORK: 

SUMMARY 

The key flaw in the document is that you arbitrarily break the landscape into three components, make the 

focus of the document on the individual discussions of those three components, and therefore make it difficult 

for you to show the inherent connectivity across these components. 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 rest of the document should be to support and 

better explain this conceptual framework. Then conceptual framework should start with the premise that all 

components of the landscape are connected, and that what differs is the degree to which they are connected 

and the importance of those connections to downstream systems. 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 should 

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 wetland or stream may be small. This, then, should 

the foundation to which you return throughout the document, always reminding the reader about how the 

supporting information in each of the three individual components relates to this conceptual model, and 

showing specifically how connections and their downstream effects are clear in some cases and not so much 

in others. 

DETAILED COMMENTS 

General Comment: Throughout the document, there were terminology 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 streams. These are often used interchangeably, even 

though they are not commonly used interchangeably, and are not defined 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 independently; 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 the case; rather, independent usage often seems to 

imply hydrological connectivity, and perhaps even surface-water 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 connectivity. 
Mark C. Rains, Ph.D. 

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General Comment: There are significant problems with some of 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 conceptual model, because it underlies the complex 

pathways and controls on hydrological connectivity. Lacking a proper conceptual framework in this regard, 

the document will fail to make a strong case not only for hydrological 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 differences in elevation (i.e., the downhill part of 

downgradient) and pressure. Pressure plays important roles in surface-water flows, but plays even more 

important roles in groundwater flows, including groundwater 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 wetland. 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 surface 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 generally include swamps, marshes, bogs, and similar 

areas.” This is very similar to a definition used later in the document (l. 3455-3456). What the authors refer to 

here is the Corps of Engineers Wetlands Delineation Manual (USACE 1987), which is guidance—which does 

not carry the full force of the law—on how to delineate a wetland and not a regulation—which does carry the 

full force of the law—on how a wetland is defined. One benefit of using the correct federal definition of a 

wetland found at 33 CFR 328.3(b)—which is more generic and inclusive, with rather vague boundaries—is 

that you won’t struggle so much in trying to explain what you 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 water in the saturated zone is under pressure and will 

rise up to the potentiometric surface if the confining layer is perforated (e.g., by a piezometer or even by a 

natural fracture, as occurs at many springs). See my comment titled “Figure 3-4”, below. 

l. 614-615: This is an inadequate definition of groundwater, because 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) groundwater and saturated-zone groundwater, respectively. 

l. 615-616: There are many saturated deposits that we do not commonly 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. 

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including low-permeability clay-rich soils, and rock has extremely low primary permeability, though it can 

have relatively high secondary permeability if there are abundant 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 connected by unconfined aquifers, but many 

others are hydrologically connected by confined aquifers, especially 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, because they are so closely related. 

There are quite a few things wrong here, which stem from an 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 Toth (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 geologic heterogeneity. Still, you might decide to 

keep this, subject to some comments below, because there’s nothing 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, however, 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 larger in spatial scale and cross one or more 

groundwater divides (i.e., they cross under one or more potential local groundwater flows). This is not the 

case in Figure 3-5; the intermediate groundwater flow is from a local high to a local low (i.e., it’s another 

local groundwater flow) while the origin of the regional groundwater flow is a bit unclear. 

Regardless, I think that this is an incomplete conceptual model of flow from uplands to rivers and wetlands. 

There actually are four pathways that water can take from an upland to a river or wetland (Figure 1; Knighton 

1998). 

• Saturated Groundwater Flow (Pathway 1 in Figure 1): This is 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 through the unsaturated zone. This is commonly 

rapid flow through preferential flow paths, which can be soil cracks, animal burrows, or naturally formed 

soil pipes. 
Mark C. Rains, Ph.D. 

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• Infiltration-Excess Overland Flow, or Hortonian Overland Flow (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 thin layer of saturation blankets the surface, and excess 

rainfall runs off. 

• Saturated Overland Flow, or Dunne’s Mechanism of Overland Flow (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 conceptual model on which to base your reasoning. This is 

particularly true, because this emphasizes an important point, which I don’t think comes through in the 

document, which is that headwaters continue from the headwater stream up to the summit of the adjacent 

hillslope. Headwater streams and adjacent hillslopes are, in fact, integrally connected, to the extent that 

headwater streams cannot exist absent the adjacent hillslopes. This point is central to the argument made by 

Nadeau and Rains (2007), and can be seen (explicitly, in some cases) in the way that they discuss the 

references therein. (See, specifically, the way they discuss 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 that there is a separate item in the list that 

comprises “at the base of a mountain”, which could be either 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 above refers to this figure. 
Mark C. Rains, Ph.D. 

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l. 720-722: You might follow this with a specific example. For example, wetlands can be seasonally isolated, 

connected by groundwater flows, and connected by surface-water and groundwater flows (Rains et al., 2006, 

2008). 

l. 794-796: A good reference for the first three items in this 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 functions 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/organic 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” includes “alluvium” and “geologic materials”, but 

alluvium is a geologic material. I suggest omitting “geologic 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 this 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 for the recruitment of vegetation, especially willows and 

cottonwoods (McBride and Strahan 1984, Scott et al., 1996, Mahoney 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 the different the different hydrographs, which 

you try to do only in the context of climate, but are, in fact, 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 true, 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 precipitation 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, but 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. Because 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. 

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l. 1194-1200, Figure 3-17: I’ve lumped the text and figure here, because 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 definition. Similarly, all aquifers are permeable, so the 

term “permeable aquifer” is redundant. Also, permeability 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 not entirely correct. However, the general themes 

in the paragraph and in the figure are not entirely incorrect, 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 correct 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 sinkhole 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 secondary 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 extreme edge of the floodplain complex, and the 

effect is that riparian/floodplain wetlands do not connect strictly 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 historic channels are reoccupied on the historic 

floodplains, can decrease the duration of dry season baseflow 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. 

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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 connections, individually or 

cumulatively, exert a strong influence on the character and functioning of downstream waters. 

a) Are these conclusions 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. 

c) Was the reviewed literature cited and summarized correctly? 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 tenets for these systems. However, I do 

have comments regarding some flaws and/or inadequacies in the 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. 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. 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 provide clearly articulated evidence, one way 

or another, toward connectivity in these contexts to better enable decision-makers to resolve this policy 

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 and ecological connectivity are central tenets of stream hydrology and 

ecology. Some examples might include the Four-Dimensional Nature of Lotic Ecosystems (Ward 1989), the 

River Continuum Concept (Vannote et al., 1980), the Serial Discontinuity Concept (Stanford et al., 1988, 

Ward and Stanford 1995, Stanford and Ward 2001), and the Featured Collection of JAWRA devoted to this 

very topic (Nadeau and Rains 2007 and references therein; Note: 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 accepted hydrological and ecological connectivity as 
Mark C. Rains, Ph.D. 

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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 paragraph. 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 explain reach-scale flow-sediment dynamics. 

Because Lane (1955) is often difficult to track down, you might also cite Bull (1991), who republished the 

findings of Lane (1955). 

l. 1977-1978: The following two comments relate to nutrient subsidies, 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 consider the following two comments here or 

elsewhere in a separate 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 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 mineralized, and 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., March–April). Thus, during the early-season storm events, there is little biological 

demand for nitrate and it is readily leached from the upland 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-fixed nitrogen subsidies in wetlands and 

streams. For example, Shaftel et 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 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 might 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. Also, Hill and Lymburner (1998) and Hill et al. (1998) did nice studies on nitrogen transformations in 

hyporheic zones, showing that even short, shallow, and fast flowpaths through the hyporheic zone are 
Mark C. Rains, Ph.D. 

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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 toward the receiving water bodies (e.g., the ocean). Nutrient spiraling is a 

way by which those nutrients 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 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 that 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 importance of anadramous fish in 

transporting nutrients, especially marine-derived nutrients, to headwater streams and associated riparian 

habitats. There is a good review of this in Nadeau and Rains (2007). 

l. 2486-2487: You might also consider adding a paragraph here on barriers 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 Soviet Union are fragmented by dams and/or 

significant water 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 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 connected with the river network, and that 

their functions exert a strong influence on the character and functioning of downstream waters. 

a) Are these conclusions 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. 

c) Was the reviewed literature cited and summarized correctly? 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 fundamental tenets for these systems. However, 

I do have comments regarding some flaws and/or inadequacies in the scientific evidence provided as 
Mark C. Rains, Ph.D. 

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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 document is unusual. I understand why you might 

want to separate this into channels, wetlands on floodplains, and wetlands not on floodplains, given the 

regulatory environment. 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 might then explain 

what kinds of wetlands might be included, using an HGM classification scheme. In this way, you can explain 

that this chapter is dealing with all kinds of wetlands—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 and ecological connectivity are 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 floodplains (Ward and Stanford 1995). Doing so will 

accomplish two objectives: (1) make it clear from the outset 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 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 floodplain wetlands. However, it 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 sediments. Riparian areas provide both short- and longterm storage locations for sediments, 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 

mobilization balance; accommodation space has been created—in which case, sediments can be stored; or 

accommodation space has been destroyed—in which case, sediments can be mobilized (Quirk 1996). 

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 better 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 discharges to riparian environments flows along regional 
Mark C. Rains, Ph.D. 

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groundwater flowpaths, and is therefore 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, have created a lot of headaches in recent years, because of 

sentences just like this, which imply that evapotranspiration causes water levels to rise. The paper, in my 

opinion, is a bit flawed, in that 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 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. 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 water table up 

toward the point. (This, in fact, is the source of the well-known capillary fringe.) The point may not be 

saturated—in fact, in most alluvial deposits, the point will 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, which 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. (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 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 

referenced 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 agricultural runoff (Peterjohn and Correll 

1984), the roles played by hyporheic flows, including those at the channel-floodplain interface, in reducing 

nitrogen in stream waters (Dahm et al., 1998, HIill and Lymburner 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 et al. (1989) developed the flood-pulse 

concept for tropical rivers; Tockner et al. (2000) extended the flood-pulse concept to temperate rivers. 
Mark C. Rains, Ph.D. 

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3. This report concludes that for non-riparian/non-floodplain wetlands that are not connected to the 

river network through a stream channel (i.e., geographically 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 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-reviewed literature on these topics, including 

evidence of connectivity and isolation? If not please indicate which references are missing. 

b) Was the reviewed literature cited and summarized correctly? 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 inadequacies 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 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 Rains (2011), who showed that moraine, ice-scour, and dead-ice 

depressional wetlands serve as groundwater recharge focal points because aeolian-transported snow is trapped 

in the topographic lows in winter and then melts and recharges underlying groundwater immediately 

following breakup in late spring, with the net effect being that groundwater recharge 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 important case of groundwater flowthrough wetlands. Groundwater flow-through lakes and depressional wetlands, where surface waters are a 

surface expression of broader groundwater phenomena, have long been recognized. Born et al. (1979) and 

Rains (2011) described groundwater flow-though depressional wetlands in glaciated landscapes, Sloan (1972) 

and Richardson et al. (1992) described groundwater flow-through prairie potholes in the northern prairie, and 

Murphy et al. (2008) described groundwater flow-through depressional 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-though wetlands supported by a seasonal perched 

aquifer that is unconnected to the underlying regional aquifers. 
Mark C. Rains, Ph.D. 

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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 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-season baseflow ceased earlier when an 

incised river was restored to the historic floodplain. One 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 connections to one another and to nearby streams. 

l. 4401-4402, l. 4415-4425: I lump these specific lines together in one comment to make an important point. 

In the first case, you state in clear, concise, and unequivocal terms that riparian and floodplain wetlands are

highly connected to river 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 systems under certain 

circumstances. You are correct; however, by dithering and then only vaguely supporting the idea that nonriparian and channel origin wetlands might be connected to river systems, and then only under certain 

circumstances, I think that you soft-peddle what we know about the flow of water across landscapes. To be 

honest, all hydrologic systems are interconnected to some degree 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 where we might choose to transition from their being a 

significant nexus to their not being 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 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 references at the end of this sentence. 

l. 5385-5387: You might consider adding Rains et al. (2006) to the references 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 perched surface-water systems; 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. 

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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 evidence? 

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 correctly? 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 streams 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 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 Preston 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 between all of the disparate pieces separately 

discussed in this 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 example, you do discuss the 

role that depressional wetlands play in storing water and 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 flood 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 typically have a step when a storm begins 

where rainfall is abstracted and put into depressional storage 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 occurring 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 and 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 case for moraine, ice-scour, and dead-ice depression in southwest Alaska. He did not 
Mark C. Rains, Ph.D. 

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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 wetlands in these environments, implying that, though 

the individual effect of one wetland may be negligible, the 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. 

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 scientific 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 hydrologic regime of glacial terrain lakes. Journal 

of Hydrology 43:7–44. 

Bull, W.B. 1991. Geomorphic Response to Climate Change. Oxford University Press, New York. 

Childers, D.L., and J.G. Gosselink. 1990. Assessment of cumulative 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 American Society of Agricultural Engineers 

38:1719–1729. 

Dynesius, M., and C. Nilsson. 1994. Fragmentation and flow regulation of river systems in the northern third 

of the world. Science 266:753–762. 

Fleckenstein, J., M. Anderson, G. Fogg, and J. Mount. 2004. Managing surface water-groundwater to restore 

fall flows in the Cosumnes River. Journal of Water Resources Planning and Management 130:301–310. 

Freeman, M.C., C.M. Pringle, and C.R. Jackson. 2007. Hydrologic connectivity and the contribution of 

stream headwaters to ecological integrity at regional scales. 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 watershed, west-central Florida, 2003-2005 

and 2009. U.S. Geological Survey Scientific Investigations Report 2010–5092. U.S. Government 

Printing Office, Washington, DC. 

Haitjema, H.M., and S. Mitchell-Bruker. 2005. Are water tables a subdued replica of the topography? Ground 

Water 43:781–786. 

Hammersmark, C.T., M.C. Rains, and J.F. Mount. 2008. Quantifying the hydrologic effects of stream 

restoration in a montane meadow environment. River Research and 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 Agricultural Engineers 11:364–367. 
Mark C. Rains, Ph.D. 

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Hill, A.R. and D.J. Lymburner. 1998. Hyporheic zone chemistry and 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. Hyporheic 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 yields for various materials. U.S. Geological 

Survey Water-Supply Paper 1662-D. U.S. Government Printing Office, 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 wetlands: 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 survival 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. Prentice-Hall, Upper Saddle River, New Jersey. 

Meyer, L.D., S.M. Dabney, and W.C. Harmon. 1995. Sediment-trapping effectiveness of stiff-grass hedges. 

Transactions of the American Society of Agricultural Engineers 38:809–815. 

Murphy, K.E., M.C. Rains, M.G. Kittridge, M. Stewart, and M.A. Ross. 2008. Hydrological connectivity 

between clay settling areas and surrounding hydrological landscapes in the phosphate mining district, 

peninsular Florida, USA. Journal of the American Water Resources 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 Resources Association 43:1–4. 

Parenteau, P. 2004-2005. Bad calls: how Corps' Districts are making 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 in an agricultural watershed: observations on the 

role of a riparian forest. Ecology 65:1466–1475. 

Pringle, C.M. 2001. Hydrologic connectivity and the management of 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. 

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Pringle, C.M. 2003b. What is hydrologic connectivity and why is it ecologically important? Hydrological 

Processes 17:2685–2689. 

Rains, M.C. 2011. Water sources and hydrodynamics of closed-basin depressions, Cook Inlet Region, Alaska. 

Wetlands 31:377–387. 

Rains, M.C., and J.F. Mount. 2002. Origin of shallow ground water 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 process 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 recharge possibilities in northwest Hillsborough County, 

Florida. U.S. Geological Survey Water-Resources Investigations 77-13. U.S. Geological Survey, 

Tallahassee, Florida. 

Sloan, C.E. 1972. Ground-water hydrology of prairie potholes in 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 microtopography 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. California 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 catchment of the upper Mississippi River. 

Journal of the American Water Resources Association 43:60–71. 
Mark C. Rains, Ph.D. 

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Ward, J.V. and J.A. Stanford. 1995. The serial discontinuity 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 frequency of forces in geomorphic processes. Journal of 

Geology 68:54–74. 
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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 endangered species recovery teams. His research on the 

effects of forestry and other land-uses on freshwater and 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. 

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Peer Review Meeting of EPA’s Draft Report: Connectivity of Streams and Wetlands to 

Downstream Waters – A Review and Synthesis of the Scientific 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 definitions 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 questioned 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, transformation 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 framework doesn’t seem to be used throughout the stream 

examples (chapter 4). For instance, the example from the prairie streams doesn’t mention these conceptual 

components much. The examples given about streams provide good examples 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 definition of riparian area as transitional between 

aquatic and terrestrial (P.26) makes it difficult to know when 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 riparian area of a navigable-in-principle stream. The 

consistent use of floodplain and riparian as a combination term (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 floodplain 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 explained 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 navigable-in-principle river, might not be covered under the 

definitions used in this report. 
John S. Richardson, Ph.D. 

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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 contributes 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 Carolina 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 little 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 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 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 waters, as expressed in the Leibowitz et al. (2008) 

paper. Moreover, the idea that these benefits may be realized or potential benefits is a helpful way to think 

about the capacity of a source system to provide benefit. However, 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 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 trying 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 staff, 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 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 subfamily 

 
John S. Richardson, Ph.D. 

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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 connections, individually or 

cumulatively, exert a strong influence on the character and functioning of downstream waters. 

a) Are these conclusions supported by the scientific evidence? 

Yes, the conclusions are consistent with the evidence presented 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 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 forested mountain landscape - Interactions of land use 

and floods. BioScience 48:681-689. 

b) Was the reviewed literature cited and summarized correctly? If not please indicate where 

correction or revision is needed. 

The review provides a solid assessment of the literature and covers the evidence for connections. Yes, the 

conclusions are supported and appropriate literature is compiled. 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 navigable-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 connected with the river network, and that 

their functions exert a strong influence on the character and functioning of downstream waters. 

a) Are these conclusions supported by the scientific evidence? 

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. 

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c) Was the reviewed literature cited and summarized correctly? 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 ensuring they point out the uncertainties in 

demonstrating significant connections. 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 floodplain differed from a riparian area, so to refer to “riparian and 

floodplain” wetlands seems redundant (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 this 

should be defined as a non-floodplain wetland. 

3. This report concludes that for non-riparian/non-floodplain wetlands that are not connected to the 

river network through a stream channel (i.e., geographically 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 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 conclusions are supported and carefully reviewed. The connection is supported for some cases, but 

not for all, so I agree that one cannot categorically conclude that this class of wetlands is connected. The 

role of isolated wetlands in 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. 

Likewise, the contributions of these isolated wetlands on transformation and storage of nutrients, 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 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 continuum, but most have evidence of some 

connection. The distinction made to clarify geographic isolation 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 state-of-the-science. 
John S. Richardson, Ph.D. 

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c) Was the reviewed literature cited and summarized correctly? If not please indicate where 

correction or revision is needed. 

The summary of the literature is very good and the authors have 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 evidence? 

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 relevant to the topic. 

c) Was the reviewed literature cited and summarized correctly? If not please indicate where 

correction or revision is needed. 

The authors have made a very thorough search of the literature for appropriate references and have drawn 

appropriate conclusions, including pointing out any uncertainties 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 there 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 would 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 “Connectivity...” 

in the report and all the workshop documentation led me to focus on the connections and not the effects. 

Given that the 1st, 2nd and 4th charge questions seem to be about consequences downstream, perhaps that 

should be better reflected in the title. It would certainly have drawn our attention more specifically to the

quantification of effects. 

As discussed in the meeting on the 30th January, the confusion over floodplain versus riparian needs to be 

clarified. Likewise, the category of non-floodplain wetlands needs more refinement as it covers an enormous 

range of wetland types. I think that if “floodplain” equals “riparian” in this scheme, then the use of floodplain 

should suffice. I found the use of “riparian” was not in line with what I consider to be riparian, but then it 

needs defining either way. 
John S. Richardson, Ph.D. 

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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 intended 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. Perhaps 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 declarative statements, such as are included in the 

charge questions. The current 6 pages of chapter 6 seems insufficient compared to the enormous detail of the 

remainder of the document. 

Here are some additional references, from those that address spatially structured populations of amphibians in 

wetlands, to papers about effects from streams to estuaries, 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 riparian areas with water. 

Additional references: 

Cole J. J., Y.T. Prairie, N. F. Caraco, W. H. McDowell, 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. Watershed effects on chemical properties of sediment 

and primary consumption in estuarine tidal flats: importance 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 British Columbia, Canada. Canadian Journal of 

Fisheries and Aquatic Sciences 65:38-46. 

Naiman, R.J., R.E. Bilby and P. Bisson. 2000. Riparian ecology and management in the Pacific coastal rain 

forest. BioScience. 50:996-1011. 

Werner E.E. et al., 2007. Turnover in an amphibian metacommunity: 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 status of amphibians. Ecology 77:2091-2097 

 DOI: 10.2307/2265703 
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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 College), 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 joining 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. Snodgrass’ current research interests include 

quantification of patterns of aquatic habitat fragmentation 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 

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Peer Review Meeting of EPA’s Draft Report: Connectivity of Streams and Wetlands to 

Downstream Waters – A Review and Synthesis of the Scientific Evidence 

Comments submitted by Dr. Joel W. Snodgrass 

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 and functioning of downstream waters. 

a) Are these conclusions supported by the scientific evidence? 

Yes, the scientific evidence clearly indicates a significant 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-reviewed literature on these topics, including 

evidence of connectivity and isolation? If not please indicate 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 headwater 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 headwater streams (Snodgrass et al., 2007; 

Peterman et al., 2009). Headwater specialists often have adaptations that allow them to cope with 

desiccating conditions 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 important component of protecting the biodiversity 

associated with our nation’s waters. The authors do acknowledge 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 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 headwater 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; Butler and Malanson, 2005) and provide habitat for numerous organisms (e.g., Snodgrass 

and Meffe 1996; Stevens et al., 2006). These hydrological and geomorphological changes have large 

impacts on ecosystem function (Naiman et al., 1996) including 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 headwater streams being places of lag and 
Joel W. Snodgrass, Ph.D. 

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transformation. This material 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 streams (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 also 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) later the authors suggest that headwater 

stream originate at where “runoff is sufficiently concentrated to erode a definable 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 channel. 

On lines 3399 through 3413 the authors summarize the effects of altered 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 species. 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 correctly? 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 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 streams. See discussion above for references. This 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 connected with the river network, and that 

their functions exert a strong influence on the character 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 zones 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 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 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. 
Joel W. Snodgrass, Ph.D. 

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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. 

To the best of my knowledge in this area the report does include the most relevant literature. However, 

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

c) Was the reviewed literature cited and summarized correctly? If not please indicate where 

correction or revision is needed. 

To the best of my knowledge in this area the report does correctly interpret and cite the literature. 

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

3. This report concludes that for non-riparian/non-floodplain wetlands that are not connected to the 

river network through a stream channel (i.e., geographically 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 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 streams are widespread and high rates of a number 

of ecological processes have been measured; therefore, these systems must have an impact on 

downstream rivers. In fact, this is a general approach that 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 extensive coverage of geographically isolated 

wetlands—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 address this issue, I think 

the argument could be made more forcefully. In fact, what 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 wetlands 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 

large impacts on streams, stream hydrology, geomorphology, ecosystem function, and biological 

communities, ultimately affecting downstream rivers (Paul and 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 no 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 wetlands have a disproportionally large influence on 

downstream waters compared to upland habitat loss. Therefore, 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 downstream streams and rivers is stronger than the 

authors indicate with this conclusion. See my general post meeting comments for further discussion of 

this issue. 
Joel W. Snodgrass, Ph.D. 

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The authors discuss “isolated wetlands that have no hydrological 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 connection to ground waters (either through 

recharge or discharge and recharge). If such studies exist 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 deep 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 groundwater 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 and similar to geographically isolated 

wetlands. 

Also related to the above comments, in the case study of Carolina bays the authors suggest that 

groundwater and surface water connections of bays to streams 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 other downstream waters.” Later (on lines 

4097-4098) the authors indicate wetlands that feed losing streams cannot be considered channel 

wetlands. However, in the previous chapter the authors argue that losing streams should be considered 

connected to more permanently flowing downstream waters. 

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 issues discussed above concerning the importance of isolation for headwater stream communities 

also applies to geographically isolated wetlands. As the authors 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 have large effects on wetland communities 

through predation, and trade-offs among the competing demands of surviving desiccating conditions and 

predation pressures creates adaptations to narrow ranges of hydrological and predator community 

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 alter biodiversity associated 

with isolated wetlands. See Snodgrass et al. (2000) for further discussion in relationship to wetland 

regulations. 

c) Was the reviewed literature cited and summarized correctly? If not please indicate where 

correction or revision is needed. 

The literature that was reviewed appears to be interpreted correctly and cited appropriately. 
Joel W. Snodgrass, Ph.D. 

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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 evidence? 

Yes the report clearly supports the idea that some wetlands and streams (if not all) make substantial 

contributions to the structure and functioning of downstream waters. 

b) Does the report include the most relevant peer-reviewed 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 correctly? If not please indicate where 

correction or revision is needed. 

Yes, again with the consideration of comments included above. 

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 floodplain wetlands and depend on overbank 

flows to connect floodplain wetlands for dispersal. 

Line 826: delete “has”—should be “This water can alter geomorphology...” 

Line 900: replace colon with period. 

Line 998: add “is”—should be “...the entire river system is difficult.” 

Lines 1445-1453: this paragraph describes a study, but does not report 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 fraction 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 streams 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. 

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Literature Cited 

Butler, D. R., and G. P. Malanson. 2005. The geomorphic influences of beaver dams and failures of beaver 

dams. Geomorphology 71:48-60. 

Brooks, R. T., and E. A. Colburn. 2011. Extent and channel morphology 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 fauna of summer-dry streams in Western 

Oregon. Archives fur Hydrobiologie 147:273-295. 

Fend, S.V., and R.O. Brinkhurst. 2000. New species of Rhynchelmis (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. Alteration of North American streams by beaver. 

BioScience 38:753-762. 

Naiman, R. J., G. Pinay, C. A. Johnston, and J. Pastor. 1994. Beaver influences on the long-term 

biogeochemical characteristics of a Boreal Forest drainage network. Ecology 75:905-921. 

Paller, M. H. 1994. Relationships between fish assemblage structure and stream order in South Carolina 

Coastal Plain streams. Transactions of the American Fisheries Society 123:150-161. 

Paul, M. J., and J. L. Meyer. 2001. Streams in the urban landscape. Annual Review of Ecology and 

Systematics 32:333–365. 

Peterman, W., J. Crawford & R. Semlitsch. 2008. Productivity and significance of headwater streams: 

population structure and biomass of the black-bellied salamander (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 Symposium 37:213-233. 

Roy, V., M. Amyot, and R. Carignan. 2009. Beaver ponds increase methylmercury concentrations in 

Canadian Shield streams along vegetation and pond-age gradients. Environmental Science & 

Technology 43:5605–5611. 

Snodgrass, J. W. 1997. Temporal and spatial dynamics of beaver-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., and 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. 

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Snodgrass, J. W., and G. K. Meffe. 1998. Influence of beavers 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 is better: beaver ponds on boreal streams as 

breeding habitat for the wood frog. Journal of Wildlife Management 70:1360–1371. 

Walsh, C. J., A. H. Roy, J. W. Feminella, P. D. Cottingham, P. M. Groffman, & R. P. Morgan. 2005. The 

urban stream syndrome: current knowledge and the search for a cure. 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 Systematics 27:337-363. 

Wiggins, G. B., R. J. MacKay, and I. M. Smith. 1980. Evolutionary 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 at the beginning of the document I think 

it would be a good idea to introduce both dimensions of time 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 isolation 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 spiraling length if the concept is applied to the entire 

gradient). Because streams and wetlands are most spatially 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 logical extension of the review to include 

the arguments presented earlier on the impacts of impervious surfaces and agricultural land conversion 

discussed in my original comments. 

On a related note to the development of the conceptual view, some changes to table 3-1 would help with 

clarity. I do like the idea of not having a specific sequence 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 large rivers. The examples I would cite here are 

adventitious streams verse true headwater streams (See Osborn and Wiley’s work that you currently cite) 

and channel wetlands along stream corridors (see Webster et 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 water 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. 

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As far as the question concerning terminology for “geographically 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 adjacent to a stream. The definition of floodplain 

wetlands would be those wetlands that occur on the floodplain 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 intent is to convey the idea that for some hillslope wetlands we do know something about connectivity, but for other we do not. 

Finally, Catherine Pringle’s work in tropical streams provides another example of the influence of 

connectivity of low-land rivers to headwater streams on community 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.. Ecology. 81:815-25. 

Crowl TA, McDowell WH, Covich AP, Johnson SL. 2001. Freshwater 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 stream. Canadian Journal of Fisheries and 

Aquatic Sciences 58: 470–478. 

March JG, Pringle CM, Townsend MJ, Wilson AI. 2002. Effects of freshwater shrimp assemblages on 

benthic communities along an altitudinal gradient of a tropical island stream. Freshwater Biology 47: 

377–390. 

Pringle CM. 1996. Atyid shrimps (Decapoda: Atyidae) influence the spatial heterogeneity of algal 

communities over different scales in tropical montane streams, Puerto Rico. Freshwater Biology 35: 

125–140. 
Joel W. Snodgrass, Ph.D. 

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Pringle CM, Blake GA, Covich AP, Buzby KM, Finley A. 1993. Effects 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 shrimp (Decapoda: Atyidae) on the depositional 

environment in a tropical stream: use of electricity for experimental 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 differences in organic matter. Ecology 80: 1860–1872. 

Riera JL, Magnuson JJ, Kratz TK, Webster KE. 2000. A geomorphic 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 within 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 Wisconsin, USA. Limnol. Oceanogr. 

41:977-984. 

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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 of Ecology, Evolution and Organismal Biology at 

Iowa State University. He has a B.Sc. in Biology from the University of Windsor, Canada; an M.Sc. in 

Botany (Plant Ecology) from the University of Alberta, Canada; and a Ph.D. in Botany (Plant Ecology) from 

North Carolina State University. Wetland vegetation dynamics, landscape differentiation within wetlands, 

and wetland restoration are his primary research interests. He has been an author or editor of 7 books on 

various aspects of wetland ecology, including three on northern 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. 

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Peer Review Meeting of EPA’s Draft Report: Connectivity of Streams and Wetlands to 

Downstream Waters – A Review and Synthesis of the Scientific Evidence 

Comments submitted by Dr. Arnold van der Valk 

This report does a very good job of reviewing the massive literature on the linkages between streams and 

wetlands and rivers. It does a particularly good job at demonstrating the linkages between streams and rivers 

and between wetlands on floodplains and rivers. It does less well in dealing with “isolated” wetlands. In large 

part this is due to lumping all kinds of non-riparian/non-floodplain 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 and 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-reviewed literature on these topics, including 

evidence of connectivity and isolation? If not please indicate which references are 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 correctly? If not please indicate where 

correction or revision is needed.

I am not an expert on hydrology, but I did not find any obvious problems 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 connected with the river network, and that 

their functions exert a strong influence on the character 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. 

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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 relevant literature on floodplains is huge and unequivocal 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 rivers and floodplains like Amoros and Bornette 

(2002). Again, I doubt that the conclusions drawn from the literature reviewed would be affected in any 

way because some relevant references were not included. 

Some relevant papers from outside NA that are missing include: 

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. 

Henry, C.P., C. Amoros, and N. Roset. 2002. Restoration ecology of riverine wetlands: a 5-year postoperation survey on the Rhone River, France. Ecological 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. Extreme 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 correctly? 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-floodplain wetlands that are not connected to the 

river network through a stream channel (i.e., geographically 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 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. This category of wetlands, however, contains a mix of wetland types that is so broad and 

heterogeneous that no definitive conclusions about their hydrological connectivity to rivers could ever be 

drawn for the entire category. There are situations where 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 types of wetlands are connected biologically to rivers 

and vice versa in many, if not all, cases. 
Arnold van der Valk, Ph.D. 

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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. 

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 are 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 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 hummocky terrain. 

c) Was the reviewed literature cited and summarized correctly? If not please indicate where 

correction or revision is needed.

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 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 evidence? 

For streams, this conclusion is self-evident and is supported 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 exactly constitutes “a cluster of small wetlands”? How do you draw the 

boundaries around a cluster? See above. 

b) Does the report include the most relevant peer-reviewed 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 correctly? If not please indicate where 

correction or revision is needed.

Yes. The problem is not with the interpretation of the literature 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. 

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Some Additional Comments 

The main purpose of this report is to demonstrate the connectivity between streams and wetlands and 

navigable rivers. There are a large number of papers that have been published in the landscape ecology 

literature on connectivity and how to measure it. This literature is largely ignored in this report. A review of 

what is meant by connectivity and the various relevant ways 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 dilemmas 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. 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 floodplains. 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 Mississippi 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 wetlands in the same class as wetlands that are the 

headwaters for streams (channel origin wetlands) is unidirectional surface flow (P. 42, ll. 813-815). Although 

some isolated wetlands like prairie potholes during high water events do have temporary surface connections 

to each other and even to nearby streams, many do not as noted. Many headwater wetlands, however, can 

have water backing up into them from streams during flooding events. It would be simpler to eliminate the 

use of the NRCW class from the report. The problem with lumping 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 wetlands. 

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 lacustrine). As defined by Cowardin et al. (1979), “The term 

SYSTEM refers here to a complex of wetlands and deepwater habitats that share the influence of similar 

hydrologic, geomorphologic, chemical, or biological factors.” Cowardin et al., recognize that intermittent 

streams are connected to perennial reaches of streams. They 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. 

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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 clearly 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 wetlands 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 the National Wetland Inventory. Discussing the 

connectivity of palustrine wetlands to rivers would make it immediately 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 function. 

What is the relative importance of hydrological vs. biological connectivity? It is possible for some types of 

wetlands to have no surface water connection to streams. Given that all wetlands have hydric plants and a host 

of aquatic animals (invertebrates, birds, mammals, microorganisms, 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 connectivity and what minimum criterion or 

threshold is required to demonstrate biological connectivity. Does demonstrating the one-time movement or 

dispersal of one species from a river or a stream to a hydrologically isolated wetland (or vice versa) mean that 

the “isolated” wetland is not really isolated? If just establishing 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 rivers, a landscape approach is needed. One 

possible way to examine these linkages would be to use an HGM 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 this general approach. The more linkages that 

can be demonstrated the greater the influence of isolated wetlands in a watershed (or other comparable 

landscape unit) on the rivers in it. 

In summary, the authors of the report focus primarily on surface water flows as the major link between rivers 

and streams and wetlands. This primarily unidirectional flow 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 influence on navigable waters has rarely been 

documented. Whether such movements are essential for the persistence 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 consequence, in any landscape all bodies of water are 

interconnected and influence each other, but these interactions are often sporadic and asymmetrical. 

A-107 

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Mark S. Wipfli, Ph.D. 

Professor 

U.S. Geological Survey Cooperative Fish & Wildlife Research 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.Sc., 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 productivity 

• Spatial subsidies in freshwater food webs 

• Linkages between freshwater-marine and freshwater-terrestrial ecosystems 

• Salmonid foraging ecology and trophic interactions 

• Invasive species impacts in freshwater/riparian ecosystems 

• Climate change effects on freshwater food webs 

• Restoration and management of freshwater and riparian ecosystems 

He has published in Canadian Journal of Fisheries and Aquatic 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, food 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 transport 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 logging effects on benthic communities? 

Hydrobiologia 641: 71-83. 

Wipfli, M.S., J.S. Richardson, and R.J. Naiman. 2007. Ecological linkages between headwaters and 

downstream ecosystems: transport of organic matter, invertebrates, and wood down headwater 

channels. Journal of the American Water Resources Association 43: 72-85. 

Gomi, T., A.C. Johnson, R.L. Deal, P.E. Hennon, E.H. Orlikowska, and M.S. Wipfli. 2006. Factors 

affecting distribution of wood, detritus, and sediment in headwater streams draining managed younggrowth red alder-conifer forests in Southeast Alaska. Canadian Journal of Forest Research 36: 725-

737. 
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Hernandez, O., R.W. Merritt, and M.S. Wipfli. 2005. Benthic invertebrate community structure in 

headwater streams is influenced by forest succession after 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 fish 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 invertebrates and detritus from fishless headwater 

streams in southeastern Alaska: implications for downstream salmonid production. Freshwater 

Biology. 47: 957-969. 
Mark S. Wipfli, Ph.D. 

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Peer Review Meeting of EPA’s Draft Report: Connectivity of Streams and Wetlands to 

Downstream Waters – A Review and Synthesis of the Scientific Evidence 

Comments submitted by Dr. Mark S. Wipfli 

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 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 supported by the evidence in the scientific 

literature. There is strong evidence in the scientific literature that headwaters are physically, biologically, 

and chemically connected to, and 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. 

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 biological linkages that may be helpful are listed 

below. The latter four deal with management effects on headwater streams. 

Wipfli, M.S., and C.V. Baxter. 2010. Linking ecosystems, food 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 detritus transport 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 influence logging effects on benthic 

communities? Hydrobiologia 641: 71-83. Addresses past timber harvest effects on headwater 

stream invertebrate communities. 
Mark S. Wipfli, Ph.D. 

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Wipfli, M.S. and J. Musslewhite. 2004. Density of red alder (Alnus rubra) in headwaters influences 

invertebrate and organic matter subsidies to downstream fish habitats in Alaska. Hydrobiologia. 

520: 153-163. This paper showed that headwater streams also supply terrestrial invertebrates to 

downstream waters, in addition to aquatic invertebrates, and illustrated 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 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 streams 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. Freshwater Biology 53: 2331–2343. 

c) Was the reviewed literature cited and summarized correctly? If not please indicate where 

correction or revision is needed. 

Yes, the literature in this report was cited and summarized 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 examples) 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 from 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. 

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2. This report concludes that open water and wetlands in riparian areas and floodplains of streams 

and rivers are physically, chemically, and biologically connected with the river network, and that 

their functions exert a strong influence on the character 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 supported by the evidence in the scientific 

literature. There is strong evidence in the 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 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. 

Yes, the report appears to include the most relevant literature 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 please indicate where 

correction or revision is needed. 

Yes, the literature in this report was cited and summarized thoroughly and correctly. 

3. This report concludes that for non-riparian/non-floodplain wetlands that are not connected to the 

river network through a stream channel (i.e., geographically 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 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? 

Question is outside my area of expertise. 

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. 

Question is outside my area of expertise. 

c) Was the reviewed literature cited and summarized correctly? If not please indicate where 

correction or revision is needed. 

Question is outside my area of expertise. 
Mark S. Wipfli, Ph.D. 

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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 evidence? 

Absolutely yes. This is a key point about headwaters and downstream waterways that unfortunately can 

easily be overlooked, and I was pleased to see this addressed. Individually, small streams do generally not 

have large influences by themselves on downstream processes, but in aggregate they tremendously affect 

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. 

Yes, the report includes the relevant scientific literature on the cumulative effects of headwaters. 

c) Was the reviewed literature cited and summarized correctly? If not please indicate where 

correction or revision is needed. 

Yes, to the best of my knowledge the literature on this topic was 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 marine-derived nutrients, and their effects on 

headwater productivity in places that receive runs of anadromous fishes. It was suggested that a discussion of 

this topic be included in the report, and I agree that it should be included. This phenomenon is demonstrated 

through runs of adult Pacific salmon throughout the west coast 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 the 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 streams, at multiple trophic levels (periphyton, aquatic 

invertebrates, and fishes). The increased production in headwaters 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 into watersheds. In turn a portion of this invertebrate 

production can subsequently get delivered downstream from headwaters. 

Here are some of my papers on this topic. They in turn contain 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 inorganic fertilizer pellets: A test on multiple 

trophic levels in streamside experimental channels. Transactions of the American Fisheries Society 139: 

824-839. 
Mark S. Wipfli, Ph.D. 

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Heintz, R.A., M.S. Wipfli, and J.P. Hudson. 2010. Identification 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 salmon rearing in beaver ponds on 

the Copper River Delta, Alaska. Canadian Journal of Fisheries 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, southcentral 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 class 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. Chaloner. 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 southeastern 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., Cederholm, C. J ., and W. J . Scarlett. 2001. Preliminary 

evaluation of the use of nitrogen stable isotope ratios to establish escapement levels for Pacific salmon. 

Fisheries 26:6-14. 

Claeson, S. M., J. L. Li, J. E. Compton, and P. A. Bisson. 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 salmon as vectors for the transfer of energy and 

nutrients between freshwater and marine environments. Freshwater Biology 48:21-27.

Nislow, K.H., and B.E. Kynard. 2009. The role of anadromous 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. Ringler, and J. G. Kennen. 1992. Factors limiting primary 

productivity in Lake Ontario tributaries receiving salmon migrations. Canadian Journal of Fisheries and 

Aquatic Sciences 49:2377-2385. 
Mark S. Wipfli, Ph.D. 

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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 another avenue thorough which headwater streams 

are connected to downstream waters. Below are a few references for the report that discuss terrestrial 

invertebrate subsidies to streams, which in turn contain further references the authors of the EPA report can 

decide on their inclusion. 

Allan, J. D., M. S. Wipfli, J. P. Caouette, A. Prussian, 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. Chapman. 2007. Invading rainbow trout usurp a 

terrestrial prey subsidy to native char and alter their behavior, growth, and abundance. Oecologia 

153:461-470. 

Baxter, C. V., K. D. Fausch, and W. C. Saunders. 2005. Tangled 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 terrestrial invertebrates to the annual resource budget 

for salmonids in forest and grassland reaches of a headwater stream. Freshwater Biology 46:303-316. 

Kawaguchi, Y., S. Nakano, and Y. Taniguchi. 2003. Terrestrial 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 terrestrial invertebrates from tree canopies to a 

stream. Freshwater Biology 12:305-311. 

Nakano, S., H. Miyasaka, and N. Kuhara. 1999. Terrestrial-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 management increases terrestrial invertebrate 

inputs that feed trout in Wyoming rangeland streams. Transactions of the American Fisheries Society 

136:1216-1230.
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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 report. Dr. Wise was unable to participate in the 

meeting and therefore was not able to prepare or submit post-meeting comments. 

William R. Wise, Ph.D. 

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Peer Review Meeting of EPA’s Draft Report: Connectivity of Streams and Wetlands to 

Downstream Waters – A Review and Synthesis of the Scientific 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 connections, individually or 

cumulatively, exert a strong influence on the character and functioning of downstream 

waters. 

a) Are these conclusions supported by the scientific evidence? 

Yes. The physical setting governs the types of material that can be transported to the downstream 

waters. This includes everything from the scale of chemicals and microorganisms to large woody debris, 

which provides important structure for a variety of aquatic species. Therefore, there is no question that 

all streams are physically, chemically, and biologically connected to the downstream waters, which 

might be rivers, estuaries, bays, springs, or aquifers. Ephemeral flow patterns should in no way be 

discriminated against because these often occur in regions where flashy events are capable of conveying 

quite a lot of matter to the receiving waters in a short period of time. Often, due to the different regime 

of the receiving water body (such as the velocity being greatly 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 are missing. 

All hydrology is local, so this is indeed a difficult question. The fact that the term karst does not appear 

in the glossary is of major concern to this reviewer. Karst 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 direct exchange mechanisms for waters and 

their physical (mostly temperature), chemical, and biological properties. One reason that this issue 

deserves special consideration is that karst features usually 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 Central Florida. It sinks into the ground and 

reemerges over three miles later. This reviewer has applied 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 consideration 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. 

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Karst systems are not unique to Florida but are prevalent in many states, such as Texas, Missouri, and 

Kentucky, to name a few. 

c) Was the reviewed literature cited and summarized correctly? If not please indicate where 

correction or revision is needed. 

The cited literature with which I had direct familiarity 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 connected with the river network, and that 

their functions exert a strong influence on the character 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 events. Their physical properties, such as 

vegetative nature and density are extremely important in governing the speed in which floods move 

through a system. 

A class of streams known as deranged, where channels flow into 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 are missing. 

Again, all hydrology is local, so this is a difficult question. The cited literature does effectively address 

the issue, however. 

c) Was the reviewed literature cited and summarized correctly? If not please indicate where 

correction or revision is needed. 

The cited literature with which I had direct familiarity was well represented. Spot checking a few others 

for personal interest verified the same. 
William R. Wise, Ph.D. 

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3. This report concludes that for non-riparian/non-floodplain wetlands that are not connected to the 

river network through a stream channel (i.e., geographically 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 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 literature and the extensive experience of this 

reviewer, who has worked in both what would be termed connected 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 are missing. 

Again, all hydrology is local, so this is a difficult question. The cited literature does effectively address 

the issue, however. 

c) Was the reviewed literature cited and summarized correctly? If not please indicate where 

correction or revision is needed. 

The cited literature with which I had direct familiarity 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 evidence? 

Yes. This is absolutely true. At any given point along a waterway, 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 question. The cited literature does effectively address 

the issue, however. 

c) Was the reviewed literature cited and summarized correctly? If not please indicate where 

correction or revision is needed. 

The cited literature with which I had direct familiarity was well represented. Spot checking a few others 

for personal interest verified the same. 

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Appendix B: Meeting Agenda 

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United States 

Environmental Protection Agency 

National Center for Environmental Assessment 

Peer Review Meeting for EPA’s Draft Report: Connectivity 

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 Organization ......................... 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; and these connections, individually or 

cumulatively, exert a strong influence on the character and functioning of downstream waters. 

a) Are these conclusions 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. 

c) Was the reviewed literature cited and summarized correctly? 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 biologically connected with the river network, and that 

their functions exert a strong influence on the character and functioning of downstream waters. 

a) Are these conclusions 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. 

c) Was the reviewed literature cited and summarized correctly? If not please indicate where 

correction or revision is needed. 
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Agenda (cont’d.) 

 12:00 PM LUNCH (on your own) 

 

 1:15 PM Charge Question 2 (discussion continues) ........................................ Walter Dodds (Chair) & Reviewers 

1:45 PM Charge Question 3 ............................................................................. Walter Dodds (Chair) & Reviewers

This report concludes that for non-riparian/non-floodplain wetlands that are not connected to the 

river network through a stream channel (i.e., geographically 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 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-reviewed 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 correctly? 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 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 evidence? 

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 correctly? 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 ADJOURN 
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Appendix C: List of Reviewers 

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United States 

Environmental Protection Agency 

National Center for Environmental Assessment 

Peer Review Meeting for EPA’s Draft Report: Connectivity 

of Streams and Wetlands to Downstream Waters - A Review 

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, FL 

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INTERNAL DELIBERATIVE MATERIALS: DO NOT DISTRIBUTE, QUOTE, OR CITE

Appendix D: List of Observers 

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INTERNAL DELIBERATIVE MATERIALS: DO NOT DISTRIBUTE, QUOTE, OR CITE

United States 

Environmental Protection Agency 

National Center for Environmental Assessment 

List of Observers

EPA 

Rebecca Aicher, AAAS Fellow, U.S. Environmental Protection Agency, Washington, DC 

Laurie Alexander, U.S. Environmental Protection Agency, 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 Agency, Washington, DC 

Rose Kwok, U.S. Environmental Protection Agency, Washington, DC 

Stephen LeDuc, U.S. Environmental Protection Agency, Washington, DC 

Jim Pendergast, U.S. Environmental Protection Agency, Washington, DC 

Amina Pollard, U.S. Environmental Protection Agency, Washington, DC 

Hadas Raanan-Kiperwas, ORISE Fellow, U.S. Environmental Protection Agency, Washington, DC 

Caroline Ridley, U.S. Environmental Protection Agency, Washington, DC 

Mark Ryan, U.S. Environmental Protection Agency, Boise, ID 

Kate Schofield, U.S. Environmental Protection Agency, Washington, DC 

Michael Slimak, U.S. Environmental Protection Agency, Washington, DC 

USACE

David Lekson, U.S. Army Corps of Engineers, Wilmington, NC 

Robert Lichvar, U.S. Army Corps of Engineers, Hanover, NH 

Karen Mulligan, U.S. Army Corps of Engineers, Washington, DC 

EPA – VIA TELECONFERENCE

Ken Fritz, U.S. Environmental Protection Agency, Cincinnati, OH 

William Kepner, U.S. Environmental Protection Agency, Las Vegas, NV 

Charles Lane, U.S. Environmental Protection Agency, Cincinnati, OH 

Michael McManus, U.S. Environmental Protection Agency, Cincinnati, OH 

Scott Leibowitz, U.S. Environmental Protection Agency, 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