Coastal Ecosystem Assessment 

of Chesapeake Bay Watersheds:

Land Use Patterns and River Conditions

December 2015

NOAA Technical Memorandum NOS NCCOS 207
Disclaimer:

This publication does not constitute an endorsement of any commercial product or intend to be 

an opinion beyond scientific or other results by the National Oceanic and Atmospheric Association 

(NOAA). No reference shall be made to NOAA, or this publication furnished by NOAA, by any 

advertising or sales promotion which would indicate or imply NOAA recommends or endorses 

any proprietary product mentioned herein, or which has as its purpose and interest to cause the 

advertised product to be used or purchased because of this publication.

Citation for this report:

Leight, A., R. Trippe III, L. Gonsalves, J. Jacobs, S. McLaughlin, G. Messick. 2015. 

Coastal Ecosystem Assessment of Chesapeake Bay Watersheds: Land Use Patterns 

and River Conditions. NOAA Technical Memorandum NOS NCCOS 207. 61pp.
Coastal Ecosystem Assessment of Chesapeake Bay 

Watersheds: Land Use Patterns and River Conditions

Leight, A.1, R.Trippe III2, L. Gonsalves 1, J. Jacobs 1, 

S. McLaughlin 1, G. Messick 1

1

NOAA, National Ocean Service

National Centers for Coastal Ocean Science

2

JHT, Inc.

NOAA Technical Memorandum NOS NCCOS 207

December 2015

United States Department

 of Commerce

Penny Pritzker

Secretary

National Oceanic and 

Atmospheric Administration

Kathryn Sullivan

Under Secretary and 

Administrator

National Ocean Service

Russell Callender

Acting Assistant 

Administrator
TABLE OF CONTENTS

EXECUTIVE SUMMARY.......................................................................................

INTRODUCTION....................................................................................................

WATERSHEDS..........................................................................................................

CORSICA RIVER..........................................................................................

MAGOTHY RIVER......................................................................................

RHODE RIVER.............................................................................................

MIDDLE RIVER...........................................................................................

SASSAFRAS RIVER.....................................................................................

NANJEMOY CREEK..................................................................................

A COMPARISON OF THE RIVERS STUDIED...................................

A CLIMATOLOGICAL NOTE.................................................................

RESULTS TEMPLATE............................................................................................

WATER QUALITY....................................................................................................

DISSOLVED OXYGEN..............................................................................

NITROGEN...................................................................................................

PHOSPHORUS..............................................................................................

SECCHI DEPTH...........................................................................................

CHLOROPHYLL A.....................................................................................

INDICATOR BACTERIA...........................................................................

LIVING RESOURCES............................................................................................

CRAB PARASITES AND HOST RESPONSES.....................................

FISH ABUNDANCE....................................................................................

FISH BODY FAT INDEX...........................................................................

EXTERNAL FISH PARASITES................................................................

FISH MACROPHAGE AGGREGATES..................................................

FISH DISEASE..............................................................................................

SUBMERGED AQUATIC VEGETATION............................................

SYNTHESIS...............................................................................................................

PARTNERS.................................................................................................................

REFERENCES..........................................................................................................

1

3

7

7

8

9

10

11

12

13

15

16

18

19

21

23

25

27

29

31

32

35

39

41

43

45

47

49

53

54
Chesapeake Bay Ecosystem Assessment Executive Summary

I

n coastal and estuarine regions, land use can have a profound impact on aquatic ecosystem health. 

In the Chesapeake Bay watershed, agriculture and urbanization have transformed major portions of 

the landscape, though some areas of undeveloped land remain. This document assesses the health 

of six Bay tributaries with different land use profiles via a suite of water quality and biological condition 

variables. Linkages are then explored between these scored variables and land use in the various 

watersheds. 

This investigation began in 2007 with three mesohaline (moderate salinity) rivers in the upper 

Chesapeake Bay, each dominated by a unique land use pattern. The Corsica, Magothy, and Rhode 

Rivers were chosen to represent systems dominated by agricultural, residential, and mixed-use lands, 

respectively. Assessment of these three rivers continued annually through 2011. From 2010 to 2012, 

three additional oligohaline (low salinity) rivers were studied. These three--the Sassafras, Middle, and 

Nanjemoy Rivers--represented the effects of predominantly agricultural, urban, and forested lands, 

respectively.

The health of each riverine ecosystem was assessed using a suite of observations focused on water 

quality and aquatic organism health. Standard water quality metrics such as dissolved nutrient 

concentrations, water clarity, and indicator bacteria loads were measured. Organismal health 

measurements included metrics of blue crab health, fish abundance, dominant fish species, fish parasites, 

fish disease, and the abundance of submerged aquatic vegetation (SAV). 

Image D1 (Disclaimer page): Submerged aquatic vegetation in the Choptank River. Image courtesy of Ben Fertig, 

Integration and Application Network, University of Maryland Center for Environmental Science (ian.umces.edu/

imagelibrary/).

Image TC1 (previous page): Aerial view of the Sassafras River. Image courtesy of Jane Thomas, Integration and 

Application Network, University of Maryland Center for Environmental Science (ian.umces.edu/imagelibrary/).

Image ES1 (above): The two Chesapeake Bay, William Preston Lane, Jr. Memorial Bridge spans emerge from fog and lowhanging clouds. Image courtesy of Kendrick Brennan, Integration and Application Network, University of Maryland Center 

for Environmental Science (ian.umces.edu/imagelibrary/).
Chesapeake Bay Ecosystem Assessment Executive Summary

Analysis of these indicators and their relationship to land use revealed patterns which provide insight 

into the trade-offs between land development and aquatic ecosystem health. This information will assist 

managers when balancing the practical requirements of a growing human population against the integrity 

of the Chesapeake Bay ecosystem.

All rivers showed some signs of stress. For example, relative to established criteria or management goals, 

most rivers contained excess nutrients (primarily phosphorus), degraded water clarity and excessive 

chlorophyll a concentrations. Poor water clarity pervaded even the forested and mixed-use watersheds. 

Another common sign of degradation was low fish diversity in all but the Rhode River, with white perch 

predominant among the species caught.

Despite the general finding of stress for all rivers, the stressors present varied by river. Excessive nutrients 

and the related effects of poor water quality and reduced benthic vegetation were detected for the two 

rivers surrounded by agriculturally-dominated watersheds, the Corsica and Sassafras. Nitrogen levels were 

particularly high in these two rivers. The agricultural systems also supported relatively high numbers of 

fish, but the health of the fish, as measured by disease prevalence and parasite loads, was much worse in 

the Corsica and slightly worse in the Sassafras than that of fish from the other rivers. Crab health was 

mixed, with high prevalence of host response detected for the agricultural systems, but relatively low 

parasite incidence.

Although results for the two rivers surrounded by large amounts of forested land (the Nanjemoy and 

Rhode Rivers) showed some signs of stress, such as excessive nutrients and poor water clarity, there were 

signs of health as well. For example, the Nanjemoy River had the highest numbers of fish and the lowest 

incidence of fish disease. The Rhode River contained the most diverse fish populations.

In addition to land use, salinity regime also grouped rivers together for certain measurements. Crab 

parasites, fish abundance, fish health and submerged aquatic vegetation scores aligned particularly well 

among rivers of similar salinities.

Differences were detected between rivers related to land use that provide information to support 

decisions regarding the control of runoff from land into the Bay. Nutrients and suspended sediments 

were important stressors in the rivers examined, supporting current Bay-wide restoration efforts 

emphasizing reductions of these compounds. Preservation of habitat to support diverse and healthy 

fish populations, especially in spawning areas, was also supported. Our findings also suggest a need to 

develop better indicators to assess the impact of crab health on population sizes and the implications for 

managing harvest. Unexpectedly, stressors in the forested and mixed-use rivers indicated that conditions 

there were less pristine than predicted, and that these areas also require management to improve 

conditions.

Image ES2: Land uses in the Chesapeake Bay watershed include forest (left), agriculture (middle), and residential 

development (right)--all part of a dynamic and inter-related ecosystem. 
Captain John Smith wrote these inspired lines during his exploration of the Chesapeake Bay in 

1608 [1]. The delicate balance of what was then a “most pleasant” pristine ecosystem is at risk 

today due to human development on a scale Smith likely never imagined. The waters of the Bay 

have become clouded, tree lines have been cut back, algae and bacteria have flourished, and many animal 

populations have dwindled.

Currently, 17 million people live in the Chesapeake 

Bay watershed, and that number is expected 

to reach 20 million by the year 2030 [2]. Many 

residents rely on the Bay and surrounding rivers 

for their livelihood—fish and shellfish in the Bay 

have supported a vibrant maritime economy since 

the 19th century. In 2012, Maryland commercial 

and recreational fisheries, and the industries they 

support, accounted for over $1 billion to the state 

economy [3]. Others make their living off of the 

land, with 25% of the watershed being devoted to 

agricultural use today [4]. Furthermore, the entire 

residential population requires living quarters as well 

as modern utilities such as paved roads and sewage 

systems. Population growth and the corresponding 

increase in exploitation of natural resources 

present many challenges to the balance of the Bay 

ecosystem.

“There is but one entrance by sea into this country, and that is at the mouth of a very 

goodly bay...All along the shores rest plenty of pines and firs...Within is a country 

that may have the prerogative over the most pleasant places known...Heaven and earth 

never agreed better to frame a place for man’s habitation.”

A Growing Problem

Chesapeake Bay Ecosystem Assessment Introduction

Image I1 (Top): Blackwater National Wildlife Refuge. 

Image courtesy of Jane Thomas, Integration and 

Application Network, University of Maryland Center for 

Environmental Science (ian.umces.edu/imagelibrary/).

Image I2 (Above): Dawn on Nanjemoy Creek.
Human land uses, such as agriculture and urban or industrial development, can impact rivers and streams 

by releasing four broad classes of contaminants: nutrients, sediments, chemical and bacterial pollutants. 

For example, land selected for farming is cleared of trees, which increases runoff, resulting in greater 

amounts of sediments in the adjacent water body. 

Fertilizers used to enhance crop production are 

mixed with runoff, causing the enrichment of the 

water body with nutrients, mainly phosphorus and 

nitrogen. Additionally, pesticides applied to protect 

crops may be flushed into adjacent waterways, where 

they can be toxic to the organisms that live there, 

including commercially important species [5]. 

Urban impervious surfaces such as roads and 

sidewalks increase runoff, bringing nutrients and 

sediments to the bay and its tributaries. Stormwater 

overflows and failing septic systems increase bacterial 

and nutrient loads in receiving waters. Industrial 

activities can magnify this problem by emptying 

chemical contaminants into those waterways [6]. 

Each of these contaminants can act as a stressor 

to fish, crabs, shellfish and their habitats, affecting 

their health and disrupting the natural balance of the 

system.

Four Classes of Contaminants

Image I3: A trash removal boat in the Baltimore Harbor. 

Image courtesy of Caroline Wicks, Integration and 

Application Network, University of Maryland Center for 

Environmental Science (ian.umces.edu/imagelibrary/).

Image I4: A NOAA scientist measures a blue crab.

Given the diversity of these contaminants and the various land uses that produce them, the Chesapeake 

Bay is an excellent case study of the relationship between land use and the health of the adjacent 

water body. The many tributaries of the Bay include urbanized, agriculturally dominated, mixeduse, and forested lands. It is therefore possible to compare widely varied land usage patterns within 

a single estuarine watershed. The Bay is also 

socially and economically valuable as a popular 

tourist destination, thriving economic center, and 

ever-expanding network of urban communities. 

Ecosystem services such as recreational and 

commercial fisheries, recreational boating, and 

ecotourism support vibrant economic sectors [3].

Why Study the Chesapeake Bay?

The Study

NOAA scientists at the Cooperative Oxford 

Laboratory (COL), in collaboration with state and 

academic partners, monitored a suite of physical 

and biological variables in six Bay tributaries from 

2007 to 2012. These tributaries featured urban, 

agricultural, forested and mixed-use watersheds, 

which were monitored for water quality and living 

resource health. Not all variables were measured in every river every year. 

Chesapeake Bay Ecosystem Assessment Introduction
8

Sampling locations were selected using a stratified 

random design. The rivers were segmented into 

branches (the smaller creeks that feed the main 

river) and three sections along the mainstem 

(Figure I1 shows an example). Water quality 

measurements were collected in spring, summer, 

and fall (between April and October) from between 

8-14 stations for each river. These water quality 

sampling locations were randomly chosen within 

each river segment using mapping software (ESRI, 

Inc.). Fish communities were sampled by both 

trawl and seine nets from each of the three main 

river segments on a monthly basis from May to 

October. Fish and crabs were collected in the fall 

(late September or early October) throughout the 

mainstem of each river for health assessments. 

The goal of this experiment was to integrate all 

of these measurements into an overall ecological 

assessment of the health of each tributary. Rivers 

with different predominant land use characteristics 

were expected to demonstrate different levels of 

Results and Synthesis ecosystem health. 

The COL published a NOAA Technical 

Memorandum in 2014 entitled “Coastal Ecosystem 

Assessment of Chesapeake Bay Watersheds-A Story 

of Three Rivers” [7]. That document integrated the 

results of sampling from 2007-2009 in the Corsica, 

Magothy, and Rhode Rivers. This document expands 

on the previous publication by providing data from 

the same three rivers in 2010 and 2011, as well as from 

three additional rivers--the Middle, Nanjemoy, and 

Sassafras--from 2010 to 2012.

Results are presented for each of the variables as a 

summary graph of the measured values and a redto-green color code for how these values compared 

to an index (see Results Template section). Wherever 

possible, the index used to evaluate condition was 

based on established criteria for the Chesapeake 

Bay or similar estuarine waters. For some variables, 

particularly those for crab and fish condition, no 

established criteria existed and the assessment of 

condition is presented as relative to the other data 

collected for this study.

Image I5: Placid waters like these belie the complex 

dynamics of ecosystem health beneath the surface.

Chesapeake Bay Ecosystem Assessment Introduction

Figure I1: Example map of a river split into sampling 

segments.
9

How to Use This Document

Each variable measured is described in a two or three page layout with standardized formatting. The 

Results Template section of the document describes the format used to assess and summarize each 

measured variable. Search the Table of Contents for variables of interest. Brief summaries of important 

trends for the variables are included at the end of each section. Finally, see the Synthesis section for 

conclusions from the assessment.

Chesapeake Bay Ecosystem Assessment Introduction

Image I7: Birds perch on a pound net in the early morning on the Corsica River.

The Road Ahead

The goals of this assessment are to characterize the conditions in the rivers studied, compare and 

contrast conditions across rivers, and to add evidence to the potential impacts of land use and human 

activities on estuarine health. The intent is to help guide community planners, local governments, 

industry, and other decision makers faced with increasing demands to make significant changes to the 

landscape. Additionally, several management implications of our findings are aimed at supporting the 

integrity of the Chesapeake Bay ecosystem. Finally, this ecological assessment of the United States’ 

largest estuary is serving as a template for a similar assessment in the Choptank River as a component of 

the Choptank Habitat Focus Area, part of NOAA’s Habitat Blueprint Program, and will help to refine 

similar approaches in other estuaries in the future. 
Chesapeake Bay Ecosystem Assessment Watersheds

Corsica River

The Corsica River runs from headwaters 

near Centreville, Maryland and empties into 

the Chester River (Figure W1). Centreville, 

situated with easy access to bay shipping, 

became a market center not long after it 

was founded in 1782 [8]. Nevertheless, 

the area never became densely populated 

and remains a rural watershed, with a 

population density ranging from 100-1,000 

people per square mile, according to the 

2010 US Census [9]. 

The watershed is dominated by farmland, 

as can be seen in Image W1. As of 2003, 

over 60% of the river’s estimated historical 

wetland area had been drained and filled to support expanded agricultural production [10].

Figure W1: Map of the Corsica River.

Overview

The Corsica River was selected for 

this study due to the high level of 

agricultural land use within its watershed. 

Furthermore, the similarity of its 

mesohaline salinity profile (generally 

between 5 and 18 parts salt per 1,000 

parts water (ppt)) to those of the 

Magothy and Rhode helps limit variation 

among the rivers to the studied variables. 

Approximately 62% of the Corsica River 

watershed is agriculture, with a small 

pocket of development at the headwaters 

where the Town of Centreville is located 

[13]. 

Study Justification

River Condition

The Corsica River has impaired conditions, due to high nutrient and sediment levels, according to the 

Maryland Department of Environment (MDE) [11]. Sampling stations along the river maintained by the 

Maryland Department of Natural Resources (MDDNR) indicate that water quality worsens upstream 

with respect to dissolved oxygen, chlorophyll a, and water clarity [12]. A wastewater treatment facility 

that once dumped directly into the river near Centreville has been redesigned to decrease nutrient and 

bacterial pollution and now applies all wastewater treatment plant discharge on land [10]. Nevertheless, 

stormwater, septic, and agricultural sources of pollution persist, and the river remains the focus of local 

conservation efforts. Ongoing nutrient pollution may be related in part to the slow leaching of nutrients 

from groundwater into the river.

Image W1: Aerial view of the Corsica River. Image courtesy of 

Jane Thomas, Integration and Application Network, University 

of Maryland Center for Environmental Science (ian.umces.edu/

imagelibrary/).
Chesapeake Bay Ecosystem Assessment Watersheds

Magothy River

Image W2: Aerial view of the Magothy River. Image courtesy of 

Ben Longstaff, Integration and Application Network, University 

of Maryland Center for Environmental Science (ian.umces.edu/

imagelibrary/).

The Magothy River flows through a 

watershed dominated by densely-packed 

single family homes. The watershed is located 

on the western shore of Chesapeake Bay in 

Maryland, south of the Patapsco River and 

north of the Severn River in Anne Arundel 

County (Figure W2). Early in its history, the 

Magothy was coveted by its residents as a 

prime waterfowl hunting area [14]. However, 

its shores became increasingly developed, 

as the area offered residents a convenient 

location near the Bay and the economic 

centers of Annapolis, Washington, and 

Baltimore. Currently, there are over 9,000 

residences with septic systems, the majority of 

these on the northern side of the river. Recreational boating is popular in the Magothy River, with over 

30 marinas and 1,700 boat docks lining the mainstem and tributary creeks. Approximately 60% of the 

shoreline has been armored with rip-rap, groins, or bulk-heading. The Magothy is larger (5,600 acres) 

and deeper (with an average depth of about 3 m) than the other two mesohaline rivers [15].

Figure W2: Map of the Magothy River.

Overview

Study Justification

River Condition

The Magothy River has impaired conditions in its tributaries due to fecal bacterial pollution, with several 

large sewage spills having occurred there in recent history. For example, Mill Creek experienced over 

three million gallons of sewage and sediment spillage in December 2005 when a corroded sewer line 

ruptured [16]. The river is also listed with the EPA as being impaired for its level of contaminants in 

fish tissues, poor benthic community 

conditions, and excessive concentrations 

of sediment and nutrients in the water 

column [11]. 

The Magothy River was chosen for this 

study due to its high level of development, 

extensive shoreline hardening, and 

numerous waste point sources. 

Additionally, it is similar in salinity range to 

the mesohaline Corsica and Rhode Rivers 

[17]. Approximately 55% of the Magothy 

River watershed is developed, with greater 

than 5% of the watershed classified as 

medium and high density development 

[13]. 
Chesapeake Bay Ecosystem Assessment Watersheds

Rhode River

Image W3: Trees line a bank of the Rhode River mainstem.

The Rhode River is a tidal tributary stretching 

three miles through Anne Arundel County 

on the western shore of the Chesapeake Bay 

(Figure W3). The landscape of the Rhode River 

was once comprised of a diverse mix of forests 

and marshlands inhabited by a large population 

of beavers. The first people known to use 

this land, the Piscataway, hunted and fished 

the region for over 2,000 years. In colonial 

times, forested land was cleared for cash crops 

including tobacco, a nutrient-depleting crop 

that demanded the continuous clearing of 

large tracts of forest. In the 1800’s, large farms 

and plantations were partitioned into smaller parcels to support more diverse crops. Wetlands were 

then ditched and drained to provide additional farmland. The long history of land use alterations in 

the Rhode River coupled with the removal of early beaver populations resulted in large amounts of 

sediment erosion from the upland areas and deposition in the stream valley, covering floodplains and 

burying historic wetlands [18]. 

Figure W3: Map of the Rhode River.

Overview

The Rhode River was selected for this study 

due to the predominance of forested land in 

its watershed. Furthermore, the similarity of 

its mesohaline salinity profile to those of the 

Corsica and Magothy helps limit variation 

among the rivers to the studied variables 

[17]. Approximately 51% of the Rhode River 

watershed is forested, with some medium 

and high density development along the 

northeastern extent of the watershed [13]. 

This balanced land use is reflected in the river’s 

diverse shorelines, from tree-lined beaches to 

waterfront homes and marinas. 

Study Justification

River Condition

Most of the Chesapeake Bay and its tidal waters are listed as being impaired and the Rhode River is no 

exception. The 2014 report card issued by West/Rhode Riverkeeper, Inc. reflects moderate to good 

scores in the Rhode River for dissolved oxygen and bacteria, a mid-level score for nutrients, poor scores 

for water clarity and chlorophyll a, and the complete absence of underwater grasses. Nearly 2,800 acres 

of undeveloped waterfront and near-waterfront lands on the Rhode River have been acquired by the 

Smithsonian Environmental Research Center since the 1960’s with the goal of protecting it from future 

development [19]. 
Chesapeake Bay Ecosystem Assessment Watersheds

Middle River

The Middle River is a wide and shallow waterway 

which runs through a heavily developed portion 

of southeastern Baltimore County (Figure W4). 

Its watershed is mainly composed of housing 

developments as well as industrial and commercial 

centers. Early in the 20th Century, population in this 

area boomed, mainly due to the jobs created by large 

corporations such as the Glenn L. Martin Company, 

Eastern Rolling Mill, and Industrial Stainless Steel, 

Inc [20]. Currently some of the larger facilities in the 

area are related to aeronautic and marine industries. 

Despite these urbanizing forces, some pockets of 

forest persist throughout the watershed, and there 

are a few rural areas near the river’s mouth [21].

Figure W4: Map of the Middle River.

Overview

The Middle River was selected for 

this study due to the high level of 

development within its watershed. 

Furthermore, the similarity of its 

oligohaline salinity profile (generally 

below 5 ppt) to those of the 

Nanjemoy and Sassafras helps limit 

variation among the rivers to the 

studied variables [17]. Approximately 

71% of the Middle River watershed 

is developed, with greater than 

23% of the watershed classified 

as medium and high density 

development [13]. 

Study Justification

River Condition

The Middle River has impaired nutrient and sediment conditions, according to MDE [11]. In March 

of 2001, Versar, Inc. submitted a report to the Baltimore County Department of Environmental 

Protection and Resource Management, citing increased levels of sediment, nutrients and heavy metals in 

the Middle River due to the amount of urbanized land within the watershed. The report recommended 

management practices to reduce future pollution loads in the river [22]. This report was adopted by 

Baltimore County as the Middle River Watershed Management Plan, under the County’s Watershed 

Management Program. Conflict has since arisen regarding the proposed development of untouched 

land within the watershed into 

residential properties [23].

Image W4: Aerial view of the Middle River, showing 

Martin State Airport. Photograph by A. Harrington, 

distributed under a Creative Commons BY-SA license.
Chesapeake Bay Ecosystem Assessment Watersheds

Sassafras River

Image W5: Aerial view of the Sassafras River. Image courtesy 

of Jane Thomas, Integration and Application Network, 

University of Maryland Center for Environmental Science (ian.

umces.edu/imagelibrary/).

The Sassafras River is a 97-square-mile 

watershed that originates in Delaware and flows 

west into Maryland, forming the northern 

boundary of Kent County (Figure W5). The 

watershed is primarily devoted to agricultural 

land use, with pockets of urban development 

and marinas. It is sparsely populated, with three 

municipalities totaling under 1,500 people. The 

Sassafras is also home to several threatened or 

endangered species, including the Puritan Tiger 

Beetle and Eastern Tiger Salamander [24].

Figure W5: Map of the Sassafras River.

Overview

Several pressing ecological issues currently 

affect the Sassafras. The river does not meet 

Federal water quality criteria for nutrients, sediment, PCBs, and organismal health [11]. MDE found that 

phosphorus was the most elevated nutrient in the river, and calculated that the river could withstand no 

more than 13,875 pounds of additional phosphorus per year and remain relatively unimpaired [25]. The 

phosphorus load in the Sassafras is currently estimated at over 20,000 pounds per year [24]. Aggressive 

vegetation like the water chestnut and various species of algae have outcompeted native species, such as 

water lilies. Algal blooms, including harmful algal blooms (HABs), block light from entering the water, 

increase eutrophication (excessive nutrients) in the water body when they decompose, and can even be 

harmful to humans [24]. Farms, lawns, leaking septic systems and other non point-sources of runoff 

have eroded the banks of the river into their characteristic cliffs of exposed clay, contributing to the 

eutrophication of the river. A major defined source of pollution is the Conowingo Dam. When this 

dam on the Susquehanna River is opened, 

outflow is caught in the mouth of the 

Sassafras and moves upriver for days, carrying 

litter and its attendant pollutants, including 

sediments [24]. 

River Condition

Study Justification

The Sassafras River was included in this 

study because of its similar salinity to the 

oligohaline Nanjemoy and Middle Rivers [17]. 

Furthermore, the river is an excellent example 

of an agriculturally dominated watershed. 

Approximately 66% of the watershed is 

devoted to agricultural use. Another 17% is 

forested, while the remaining fifth is a mixture 

of wetland and developed land [13].
15

Chesapeake Bay Ecosystem Assessment Watersheds

Nanjemoy Creek

The Nanjemoy Creek is a mostly 

forested watershed [26] 13.1 miles in 

length [27] which empties into the 

Potomac River about 25 miles south 

of Washington DC (Figure W6). 

Narrow, long tributary creeks wind 

through the hilly watershed and end 

in a relatively wide and shallow creek 

mouth. Of the watersheds’ nearly 

50,000 acres, roughly 150 landowners 

account for over 75% (about 25,000 

acres) of the unprotected land [26]. 

The Nature Conservancy works to 

preserve the remaining area, which 

is mostly forested, with the initial 

goal of maintaining a breeding ground 

for great blue herons, but now with the goal of sheltering a fully functional forest ecosystem [26]. The 

watershed is also home to the Nanjemoy Creek Environmental Education Center, which focuses on 

teaching local students about environmental science [28]. 

Image W6: Sunrise on the Nanjemoy. 

Overview

River Condition

According to a 2013 document prepared by the Chesapeake Bay Foundation, only 2% of the Nanjemoy 

watershed has been converted to impervious surfaces. The document cites this as a major reason 

for the Creek’s good water quality and low polluted runoff loads [29]. Nevertheless, MDE has listed 

the Nanjemoy waterway as 

impaired due to such pollutants 

as nutrients and suspended 

sediments [11].

Study Justification

The Nanjemoy was included 

in the current study due to 

the low level of development, 

predominance of forested lands, 

and emphasis on preservation 

in the watershed. In addition, its 

salinity profile is closely matched 

to those of the oligohaline 

Middle and Sassafras Rivers [17].

Figure W6: Map of Nanjemoy Creek.
Chesapeake Bay Ecosystem Assessment Watersheds

A Comparison of the Rivers Studied

Figure W7. The six watersheds, color coded by land cover types, by location in the Chesapeake Bay. The main variables 

used in selecting the watersheds for this study were land cover classifications and salinity regime. Scale bars are included 

with each watershed projection in order to judge relative size. The largest watershed was that of the low salinity Sassafras 

which, along with the brackish water Corsica River watershed, consists primarily of agricultural lands and is located on 

the Eastern Shore (i.e. east of the Chesapeake Bay). The Middle and Magothy Rivers, study sites which were chosen 

due to their high levels of commercial and residential development, reside along the heavily developed Washington and 

Baltimore corridor. The smallest watershed was the Rhode. Along with the Nanjemoy watershed, it is located in the more 

rural and undeveloped lands on the Western Shore in southern Maryland [13].
Chesapeake Bay Ecosystem Assessment Watersheds

Watershed Facts

River Corsica Sassafras Magothy Middle Rhode Nanjemoy

Primary Land Use Agricultural Urban Forested/Mixed Use

Average Depth (m) 1.978 2.81 2.90 1.57 1.59 0.97

303d Impairments*

PCB

FC

TSS

N

P

PCB

FC

TSS

N

P

BIBI 

PCB

FC

TSS

N

P

PCB

TSS

N

P

FC

N

P

BIBI

TSS

N

P

Hardened Shoreline (%) 15 9 60 51 25 4

Watershed Area Except 

River (acres) 23,900 53,700 20,900 6,100 8,700 46,700

River Area (acres) 1,400 8,300 5,600 2,400 1,200 2,700

River:Watershed Ratio 1:17 1:6 1:4 1:3 1:7 1:17

Figure W8: This graph shows the average depth of the 

rivers studied. The error bars represent 95% confidence 

limits.

Table W1: This table provides details and comparisons of the six rivers examined in this study with regards to known 

impairments [11], differences in shoreline habitats, average depths, river areas, and watershed areas [15]. All six rivers 

contain excessive nutrients, as assessed by the MDDNR and the MDE [11]. 

*BIBI = Benthic Index of Biotic Integrity; PCB = Polychlorinated Biphenyls; FC = Fecal Coliforms; TSS = Total 

Suspended Solids; N = Nitrogen; P = Phosphorus.

0

2

4

6

8

10

12

Corsica Sassafras Magothy Middle Rhode Nanjemoy

Salinity (ppt)

River

Average Salinity

0

0.5

1

1.5

2

2.5

3

3.5

4

Corsica Sassafras Magothy Middle Rhode Nanjemoy

Depth (m)

River

Average River Depth

Figure W9: This graph shows the average salinity of the 

rivers studied. The error bars represent 95% confidence 

limits.
Chesapeake Bay Ecosystem Assessment Watersheds

A Climatological Note

Climate can have a distinct impact on conditions in coastal 

waters. Changes in air temperature and precipitation have 

been linked to changes in nutrient levels [30], dissolved 

oxygen levels in bottom waters [31], zooplankton 

populations [32], fish populations [33], and fecal bacteria 

in surface waters [34]. Some of these relationships, such as 

with striped bass population size, consist of multi-decadal 

cycles, which are much longer than the scope of the six 

watersheds study. Other components of the estuarine 

ecosystem, such as nutrient loads and water clarity, are 

influenced by annual climate variability and within-year 

timing of precipitation and air temperature changes. In 

order to provide contextual climate information for the six 

watersheds study, air temperature and precipitation values 

in the Chesapeake Bay are presented (Figure W11).

Climate data was collected from the 

National Climatic Data Center [35] using 

Climate Division information from the 

Chesapeake Bay region (Figure W10). This 

data is quality assured and presented by 

geographic area as monthly averages (air 

temperature) or totals (precipitation).

For the years of this study, precipitation 

ranged from a fairly dry year in 2007 to an 

unusually wet year in 2011 (Figure W11). 

The extreme precipitation events in 2011, 

reflected in the large error bars that year, 

occurred in August and was related to 

Hurricane Irene.

Average annual temperatures also showed 

some interannual varibility, though not with 

a consistent trend over the six years and 

not with the same pattern as precipitation.

Figure W10: This map shows the climate divisions 

surrounding the Chesapeake Bay used for climate 

data in this study.

Figure W11: These graphs show average monthly temperature (top) 

and precipitation (bottom) for the six years of this study. Error bars 

represent 95% confidence limits. 

55

60

65

70

75

80

2007 2008 2009 2010 2011 2012

Temperature (◦F)

Year

Monthly Air Temperature

25 Year

Average

0

1

2

3

4

5

6

7

8

2007 2008 2009 2010 2011 2012

Precipitation (in)

Year

Monthly Precipitation

25 Year

Average
Chesapeake Bay Ecosystem Assessment Results Template

Figure RT1: Bar charts of this type compare assessment variables 

between rivers, in their original units. If two bars do not share any 

of the same white letters, then they are significantly different. The 

error bars display 95% confidence limits, which provide a relative 

estimate of differences between average conditions for the six 

rivers, but not an absolute measure of significance. An Analysis 

of Variance (ANOVA) test was performed for each variable, often 

after transforming the data, in order to assess differences between 

rivers.

Figure RT2: Tables like the one above explain how measured 

values were translated into scores for the variable assessed. In 

this example, dissolved oxygen criteria are differentiated by 

river habitat and time of year. All measurements meeting or 

exceeding these criteria were scored a 5, while measurements 

below were scored a 1. The scoring methodology and 

relevant literature references are further described in the text 

accompanying each variable.

Dissolved Oxygen Criteria

Habitat Criteria (mg/L) Time of Year

Open Water ≥5.0 Year-Round

Deep Water ≥3.0

≥5.0

Jun. 1 - Sep. 30

Oct. 1 - May 31

Deep Channel ≥3.0

≥5.0

Jun. 1 - Sep. 30

Oct. 1 - May 31

3

4

5

6

7

8

9

Corsica Sassafras Magothy Middle Rhode Nanjemoy

Dissolved Oxygen, mg/L

River

Dissolved Oxygen in Surface Waters

A A A A A B

This section describes the presentation of results throughout the document 

and how to read the figures that will be displayed for each of the variables 

investigated for this assessment.
Chesapeake Bay Ecosystem Assessment

1 s 2 s 3 s 4 s 5 

S

C

Ma

Mi

R

N

Figure RT5: The spectrum above represents the variable score (from 1 as poor condition to 5 as good 

condition). The initials of each river are overlaid on the spectrum representing the average score over 

all years. The error bars represent one standard deviation from the mean. If the standard deviation is 

very small no bars appear. 

Figure RT4: The table above is a heat map representing the scores for each river by year. The colors 

are chosen from the color bar in Figure RT5, based on the corresponding score.

River

Corsica

Sassafras

Middle

Magothy

Rhode

Nanjemoy

Mi

Ma

C

R

S

N

Abbr 2007 2008 2009 2010 2011 2012

Results Template

Score Equivalence for Total Nitrogen

Score 1 3 5

Criteria (uM) ≥92 ≥46 and <92 <46

Figure RT3: In a variation of the table in Figure RT2, the table above shows how nitrogen was 

scored. The score calculations were not broken down by any sub-criteria here; rather, the scoring 

criteria was the same for all measurements. Measurements in each category were thus assigned the 

corresponding score.

Findings

• Bullet points here summarize the results shown in bar charts, heat map and red-to-green 

scoring spectrum.
The term ‘water quality’ generally refers to the set of physical, chemical, and biological conditions 

of a water body that affect its ability to support particular uses [36]. Often, water quality is 

assessed with respect to human needs, such as drinking water and recreational activities like 

swimming. In this study, we assessed the condition of the water in six rivers relative to established 

criteria and to published goals that represent conditions necessary to support healthy communities 

of organisms. Focusing on a few factors, including concentrations of dissolved oxygen, nitrogen, 

phosphorus, chlorophyll a, fecal indicator bacteria, and measurements of water clarity, this assessment 

sought to provide an accurate indicator of water quality in the six rivers that were investigated. 

In addition to the variables listed above, water temperature and salinity were measured every half meter 

in depth at each sampling station. These two variables may be informative on their own, are necessary 

for calculating several of the indicators, such as dissolved oxygen conditions, and add contextual 

information for comparison of the rivers. Average salinity conditions were presented in the Watersheds 

section (Figure W9). Water temperatures did not differ substantially among the rivers, averaging between 

23 and 25 °C. 

Many factors influence water quality, from hurricanes to wastewater effluent. General trends in water 

quality may also be associated with land use practices, such as eutrophication (i.e. excess nutrients) in 

agricultural areas and decreased water clarity in areas of sediment runoff [37-39]. One goal of this study 

was to look for trends in these water quality parameters in relation to the various potential drivers in 

each river.

Chesapeake Bay Ecosystem Assessment Water Quality

Image WQ1: Boats on the Chesapeake Bay. Image courtesy of Jane Hawkey, Integration and Application Network, 

University of Maryland Center for Environmental Science (ian.umces.edu/imagelibrary/).
Dissolved Oxygen

In natural water bodies, oxygen is diffused from the overlying atmosphere and mixed into the water 

column by wind and waves. Oxygen is also produced by plants and some bacteria and is a requirement 

of most aquatic organisms. Therefore, dissolved oxygen levels play perhaps the most significant role in 

determining what species can survive in a given body of water [40].

Dissolved oxygen may become depleted in bottom waters when the water column exhibits stratification 

(strong horizontal layering), excess nutrients, or both [40]. In large estuaries such as the Chesapeake Bay, 

stratification of the water column occurs in the mainstem and lower portions of some tributaries in 

late spring through late summer as water temperatures increase and storm frequencies decrease. Most 

water quality assessments, including the USGS National Water Quality Assessment Program [41] and 

Chesapeake Bay Report Card [42], account for seasonal variation in dissolved oxygen concentrations.

Background

Methods

Average dissolved oxygen levels (mg/L), for 

both surface and bottom waters, are shown 

in Figure WQ1. The US EPA has suggested 

levels of dissolved oxygen sufficient to 

support aquatic life in each sub-habitat, for 

each season, within the Chesapeake Bay 

[43]. These sub-habitats and their associated 

seasonal dissolved oxygen criteria are 

presented in Figure WQ2. 

For this assessment, dissolved oxygen levels 

were measured at 0.5 meter depth increments 

at each station. Levels were measured as 

concentrations in milligrams of oxygen 

per liter of water (mg/L). Stratified waters, 

if present, were calculated as described by 

the Chesapeake Bay Program [44], and the 

appropriate EPA dissolved oxygen criteria 

were applied to evaluate condition. 

If a measurement exceeded the criteria it 

was scored as a 5; if not, it was scored as a 1. 

Scores at the stations were averaged for each 

river by year (Figure WQ3) and then averaged 

for each river for all years sampled (Figure 

WQ4). Data were analyzed with respect to 

river, year, and depth.

Figure WQ1: Average dissolved oxygen concentrations in surface 

(top) and bottom (bottom) waters for each river studied.

Chesapeake Bay Ecosystem Assessment Water Quality

3

4

5

6

7

8

9

Corsica Sassafras Magothy Middle Rhode Nanjemoy

Dissolved Oxygen, mg/L

River

Dissolved Oxygen in Surface Waters

A A A A A B

3

4

5

6

7

8

9

Corsica Sassafras Magothy Middle Rhode Nanjemoy

Dissolved Oxygen, mg/L

River

Dissolved Oxygen in Bottom Waters

B A C B B B
Results

Dissolved Oxygen Criteria

Habitat Criteria (mg/L) Time of Year

Open Water ≥5.0 Year-Round

Deep Water ≥3.0

≥5.0

Jun. 1 - Sep. 30

Oct. 1 - May 31

Deep Channel ≥3.0

≥5.0

Jun. 1 - Sep. 30

Oct. 1 - May 31

Figure WQ4: Overall dissolved oxygen scores for each river. Error bars represent one standard deviation from the 

mean of all annual scores.

Chesapeake Bay Ecosystem Assessment Water Quality

Figure WQ3: Heat map of dissolved oxygen scores by river and year. 

Figure WQ2: Threshold criteria for dissolved oxygen by estuarine 

sub-habitat and time of year.

Dissolved Oxygen Findings

• Dissolved oxygen was generally sufficient to support natural resources in all six rivers, which 

is in agreement with the Chesapeake Bay Report Card [42].

• The Magothy and Nanjemoy had lower dissolved oxygen measurements than the other rivers, 

though their scores were still acceptable.

• Dissolved oxygen concentrations in bottom waters of the Magothy were lower than all other 

rivers and insufficient to support benthic organisms at times.

• Interannual variability and trends were minimal.

River

Corsica

Sassafras

Middle

Magothy

Rhode

Nanjemoy

Mi

Ma

C

R

S

N

Abbr 2007 2008 2009 2010 2011 2012

1 s 2 s 3 s 4 s 5 

S

C

Ma

Mi

R

N
Nitrogen is an essential nutrient 

for all organisms. It enters aquatic 

systems primarily through atmospheric 

deposition, stormwater runoff and 

groundwater flows. However, if nitrogen 

concentrations become excessive (and 

sufficient amounts of phosphorus 

are also present, a process called 

eutrophication), estuarine plants and 

bacteria grow at stimulated rates, which 

can lead to overproduction. For example, 

in the Chesapeake Bay, high nitrogen 

concentrations often cause phytoplankton 

blooms in surface waters during spring 

and summer [45,46]. 

Overproduction causes problems 

for an estuarine ecosystem. When 

phytoplankton blooms die, they sink 

to the bottom and are consumed by bacteria. These bacteria use up dissolved oxygen, leading to low 

oxygen concentrations in bottom waters. These conditions are exacerbated by stratification of waters 

that often occur in areas of the Bay during hot summer months. In this way, concentration of nutrients 

such as nitrogen in the water are important indicators of water quality and habitat condition [46].

Nitrogen

Image WQ2: This graphic demonstrates nitrogen cycling through a 

riverine ecosystem and the associated watershed. Image courtesy of 

Catherine Ward, Integration and Application Network, University 

of Maryland Center for Environmental Science (ian.umces.edu/

imagelibrary/).

Background

Methods

Water samples for nitrogen analysis were collected just below the surface using acid-washed 500 mL 

plastic bottles. In order to compare 

nitrogen concentration in the samples 

with established water quality criteria 

[47], inorganic and organic nitrogen 

compounds, in both dissolved and 

particulate forms, were measured 

using analytical instruments [48] and 

combined to establish a total nitrogen 

concentration. Average concentrations 

are shown in Figure WQ5. Total 

nitrogen values were then compared 

to an established threshold (46 μM) 

for the health of seagrass beds [47], 

and a value double that level (92 μM) 

reflective of extreme concentrations 

Figure WQ5: Average nitrogen concentrations for each of the studied (Figure WQ6).

rivers.

Chesapeake Bay Ecosystem Assessment Water Quality

0

20

40

60

80

100

120

Corsica Sassafras Magothy Middle Rhode Nanjemoy

Nitrogen (uM)

River

Nitrogen

A B C D C C
Figure WQ8: Overall nitrogen scores for each river. Error bars represent one standard deviation from the mean of 

all annual scores.

Results

Score Criteria for Total Nitrogen

Score 1 3 5

Criteria (μM) ≥92 ≥46 and <92 <46

Chesapeake Bay Ecosystem Assessment Water Quality

Figure WQ6: This table classifies the threshold levels of nitrogen for each 

score.

Figure WQ7: Heat map of nitrogen scores by river and year.

River

Corsica

Sassafras

Middle

Magothy

Rhode

Nanjemoy

Mi

Ma

C

R

S

N

Abbr 2007 2008 2009 2010 2011 2012

1 s 2 s 3 s 4 s 5 

S

C

Ma

Mi

R

N

Nitrogen Findings

• Concentrations of nitrogen were statistically highest in the agricultural Corsica, followed by 

the agricultural Sassafras, and lowest in the urban Middle River (Figure WQ5).

• Similarly, nitrogen scores were also worse in the two agriculturally dominated rivers, especially 

the Corsica, and best in the more heavily developed rivers, Middle and Magothy (Figure 

WQ8).

• No significant chronological patterns were observed. Varying rainfall totals did not seem to 

affect annual nitrogen levels at the spatial scale of this study.
In addition to nitrogen, all organisms depend 

on external sources of phosphorus. Although 

phosphorus compounds occur naturally in 

most aquatic systems, many estuaries suffer 

from excessive phosphorus input due to human 

activities, via agricultural application, wastewater 

treatment and urban runoff. Erosion and overground runoff are responsible for more than half 

of the phosphorus transported into Chesapeake 

Bay [46,49].

Overloading a water body with phosphorus 

causes problems similar to the effects of nitrogen 

pollution. Both nutrients are consumed by 

algae which can then grow into “blooms” that 

cover the surface of the water body, preventing 

sunlight from reaching other aquatic vegetation. 

Furthermore, when the algae dies, it sinks to the 

bottom where it is consumed by bacteria, which 

use dissolved oxygen in bottom waters, causing 

hypoxia (low oxygen) and anoxia (no oxygen). 

These poor conditions can be dangerous and even 

lethal to fish and shellfish [46].

Phosphorus

Figure WQ9: Average phosphorus concentration in each studied river.

Background

Methods

Water samples for phosphorus 

analysis were collected from just 

below the surface using acidwashed 500 mL plastic bottles. 

Total phosphorus, consisting of 

both dissolved and particulate 

forms, were measured using 

analytical instruments [48]. 

Average concentrations are shown 

in Figure WQ9. Total phosphorus 

values were then compared to an 

established threshold (1.2 μM) 

for the health of seagrass beds 

[47], and a value double that level 

(2.4 μM) reflective of extreme 

concentrations (Figure WQ10).

Chesapeake Bay Ecosystem Assessment Water Quality

0

1

2

3

4

5

6

7

Corsica Sassafras Magothy Middle Rhode Nanjemoy

Phosphorus (uM)

River

Phosphorus

A C D C C B

Image WQ3: A NOAA scientist collects a water sample for 

chlorophyll a and nutrient analysis.
Results

Score Criteria for Total Phosphorus

Score 1 3 5

Criteria (μM) ≥2.4 ≥1.2 and <2.4 <1.2

Chesapeake Bay Ecosystem Assessment Water Quality

Figure WQ10: Threshold levels of phosphorus and their corresponding scores.

Figure WQ11: Heat map of phosphorus scores by river and year.

Figure WQ12: Overall phosphorus scores for each river. The error bars represent one standard deviation.

Phosphorus Findings

• Concentrations of phosphorus were highest in the agricultural Corsica, followed by the 

forested Nanjemoy (Figure WQ9)

• The urban Middle and forested Nanjemoy Rivers had surprisingly high phosphorus 

concentrations. 

• Low index scores were found for all rivers, with Magothy scoring the highest (Figure WQ12).

• As with nitrogen, the agricultural rivers scored poorly relative to most other rivers.

• Scores degraded over time in the Sassafras, Magothy and Middle Rivers (Figure WQ11).

River

Corsica

Sassafras

Middle

Magothy

Rhode

Nanjemoy

Mi

Ma

C

R

S

N

Abbr 2007 2008 2009 2010 2011 2012

1 s 2 s 3 s 4 s 5 

S

C

Ma

Mi

R

N
0

0.2

0.4

0.6

0.8

1

Corsica Sassafras Magothy Middle Rhode Nanjemoy

Depth (m)

Secchi Depth

A A B A,C C D

Many organisms, 

such as plants and 

photosynthetic bacteria, 

use sunlight as their 

source of energy. 

Water clarity, which 

is a function of the 

depth that light of 

various wavelengths can 

penetrate into a water 

body, is therefore an 

important indicator of 

the water quality and 

overall condition of an 

aquatic ecosystem [50]. 

Water clarity is affected 

by many variables, but is 

primarily related to the 

amount of suspended 

material in the water. This material can be living organisms (e.g. phytoplankton), organic debris, or 

inorganic particles [50-51].

Secchi Depth

Figure WQ13: Average Secchi depth for each of the studied rivers.

Background

Methods

Water clarity was estimated by Secchi depth measurements. The Secchi disk is a small flat disk with 

alternating black and white painted quadrants (Image WQ4), and is used widely to assess water clarity. 

The disk is lowered into the water until the pattern on the disk is no longer visible. This measurement 

is called Secchi depth and provides 

an estimate of turbidity. Because 

readings are affected by sun angle, 

cloud cover and other lighting 

factors, care must be taken to 

minimize sampling biases. Average 

Secchi depths in the six rivers 

are presented in Figure WQ13. 

Individual measurements were 

then compared to the published 

thresholds of 0.65 m (oligohaline 

waters) and 1.63 m (mesohaline 

waters) for phytoplankton health 

in Chesapeake Bay [52] (Figure 

WQ14). 

Image WQ4: A NOAA scientist watches until the black and white segments on the secchi 

disk are indistinguishable under water (left) and then reads the depth at that point (right).

Chesapeake Bay Ecosystem Assessment Water Quality
Results

Chesapeake Bay Ecosystem Assessment Water Quality

Figure WQ14: Secchi depth scoring criteria by salinity profile.

Figure WQ16: Overall scores for each river. Error bars represent one standard deviation.

Figure WQ15: Heat map of scores by river and year.

Score Criteria for Secchi Depth

Score

Habitat 1 3 5

Oligohaline (salinity <5.0 ppt) ≤0.325 m >0.325 m and ≤0.65 m >0.65 m

Mesohaline (salinity >5.0 and <18 ppt) ≤0.815 m >0.815 m and ≤ 1.63 m >1.63 m

Secchi Depth Findings

• The forested Nanjemoy unexpectedly had the worst average water clarity (Figure WQ13), 

perhaps because it is a shallow river with fine benthic sediments and has a very large watershed 

relative to river size.

• The Magothy had deepest Secchi readings, though the scoring criteria still indicated poor water 

clarity (Figure WQ16).

• Except for the Nanjemoy, the oligohaline rivers (Sassafras and Middle) scored better than the 

mesohaline rivers (Rhode, Magothy, and Rhode), partly due to the salinity-dependence of the 

scoring criteria.

River

Corsica

Sassafras

Middle

Magothy

Rhode

Nanjemoy

Mi

Ma

C

R

S

N

Abbr 2007 2008 2009 2010 2011 2012

1 s 2 s 3 s 4 s 5 

S

C

Ma

Mi

R

N
The pigment chlorophyll a plays a critical 

role for most photosynthetic organisms: 

it captures light, which supplies necessary 

energy for plants and some bacteria to 

produce organic molecules. Chlorophyll 

a concentrations can be measured to 

attain an estimate of the density of 

photosynthetic organisms in natural 

waters. The presence of low to moderate 

levels of chlorophyll a suggests a healthy 

habitat where primary producers, in 

balance with consumers, are creating 

organic matter from inorganic molecules 

and producing oxygen as a waste product. 

However, high levels of chlorophyll a indicate the presence of excess nutrients, favorable temperatures, 

and the necessary salinity conditions to support the growth of dense phytoplankton populations [53]. 

Habitat loss, reduced growth rates, or disturbances in trophic structure may result in system 

imbalances with high levels of chlorophyll a present, as phytoplankton growth outpaces phytoplankton 

consumption by grazers such as zooplankton. Stratification of waters in warm summer months 

concurrent with high phytoplankton growth rates establish conditions for low dissolved oxygen in 

bottom waters and reduced habitat for 

aerobic organisms.

Chlorophyll a

Background

Methods

Chlorophyll a was measured in surface 

water samples by filtering 50-100 mL 

of water through a pre-rinsed 0.7 um 

filter. The filters were stored on dry ice 

in the field and in a -80°C freezer in the 

lab. Chlorophyll a concentrations were 

measured from the filters using high 

performance liquid chromatography 

[48]. Average conditions for each 

river are presented in Figure WQ17. 

Individual measurements were 

compared to an established threshold 

[47] for the health of seagrass beds (15 

μg/L), and a value double that level 

(30 μg/L) reflective of extremely high 

concentrations.

Image WQ5: Algal blooms such as this denote an imbalance in the 

production of photosynthetic organisms and their consumption. 

Image courtesy of Jane Thomas, Integration and Application Network, 

University of Maryland Center for Environmental Science (ian.umces.edu/

imagelibrary/).

Chesapeake Bay Ecosystem Assessment Water Quality

0

10

20

30

40

50

60

70

80

Corsica Sassafras Magothy Middle Rhode Nanjemoy

Chlorophyll 

a (uM)

River

Chlorophyll a

A A B C B B,C

Figure WQ17: Average concentrations of total chlorophyll a in the rivers 

studied.
Results

Score Criteria for Chlorophyll a

Score 1 3 5

Criteria (μg/L) ≥30 ≥15 and < 30 <15

Chesapeake Bay Ecosystem Assessment Water Quality

Figure WQ19: Heat map of chlorophyll a scores by river and year.

Figure WQ20: Overall chlorophyll a scores by river. Error bars represent one standard deviation.

Figure WQ18: Criteria for chlorophyll a values (based on [46])

and their corresponding scores.

1 s 2 s 3 s 4 s 5 

S

C

Ma

Mi

R

N

River

Corsica

Sassafras

Middle

Magothy

Rhode

Nanjemoy

Mi

Ma

C

R

S

N

Abbr 2007 2008 2009 2010 2011 2012

Chlorophyll a Findings

• Agricultural rivers (Corsica and Sassafras) had predictably high concentrations (Figure WQ17) 

and low scores (Figure WQ20) for chlorophyll a.

• The urban Magothy and less developed Nanjemoy and Rhode had similar chlorophyll a

concentrations, while the urban Middle had the lowest concentrations.

• The Sassafras, despite better nutrient scores than the Corsica, scored slightly worse for 

chlorophyll a.

• The Middle and Nanjemoy had relatively low chlorophyll a concentrations and the best scores.

• All rivers became more degraded over the course of the study.
An important component of 

water quality is the presence and 

concentration of human pathogens. 

Humans may contract an illness 

from estuarine environments via 

direct contact with the polluted 

water or from the consumption of 

raw or undercooked contaminated 

shellfish. Monitoring water bodies 

for potential pathogens is infeasible 

due to their great diversity. However, 

fecal bacteria like Enterococcus spp. are 

good indicators of human pathogen 

levels. That is, although fecal 

bacteria are not usually harmful, their concentrations may correspond to risk of encountering pathogenic 

bacteria [54]. Therefore, fecal bacteria are often monitored in both fresh and marine waters as well as in 

seafood to indicate the likelihood of contracting human illness from contact with those waters or food 

items.

Indicator Bacteria

Figure WQ21: Percent of indicator bacteria measurements for each river that 

exceed the EPA criteria for a healthy river.

Background

Methods

For this study, Enterococcus spp. bacteria 

concentrations were measured in all six studied 

rivers. Bacteria were isolated using standard 

methods [55], which involve filtering sample 

water, incubating filters on specific culture 

media, counting bacteria colonies on the media, 

and comparing the counts to threshold criteria 

determined by the EPA. For marine and estuarine 

waters, the US EPA has established that waters 

with concentrations below 104 cells/100 mL are 

acceptable as “designated beach areas”, and that 

waters with concentrations below 158 cells/100 

mL are acceptable for “moderate” swimming 

use [56]. Although samples for this study were 

not collected at beaches, these criteria represent 

reasonable indicators of risk due to recreational 

activities in estuarine waters [24,57-61]. The 

“designated beach area” criterion was used as a 

lower threshold and the “moderate” swimming 

use criterion was used as an upper threshold in 

Image WQ6: Indicator bacteria were counted according to this study.

standard methods[54], by placing filters on growth media.

Chesapeake Bay Ecosystem Assessment Water Quality

0

20

40

60

80

100

Corsica Sassafras Magothy Middle Rhode Nanjemoy

Percent Over EPA Criteria

River

Percent of Indicator Bacteria Samples Over 

EPA Criteria

A A A A A B
Results

Score Criteria for Indicator Bacteria

Score 1 3 5

Criteria (colonies/100 mL) ≥158 ≥104 and < 158 <104

Chesapeake Bay Ecosystem Assessment Water Quality

Figure WQ22: Criteria for indicator bacteria colony densities [56] and their 

corresponding scores.

Figure WQ23: Heat map of scores by river and year.

Figure WQ24: Overall scores by river. Error bars represent one standard deviation.

River

Corsica

Sassafras

Middle

Magothy

Rhode

Nanjemoy

Mi

Ma

C

R

S

N

Abbr 2007 2008 2009 2010 2011 2012

1 s 2 s 3 s 4 s 5 

S

C

Ma

Mi

R

N

Indicator Bacteria Findings

• There were no discernable trends in bacteria levels due to land use or climate.

• The predominantly forested Nanjemoy had the highest concentrations of indicator bacteria 

(Figure WQ21), corresponding to poor water clarity and high suspended sediment levels.

• The agricultural Corsica had the next highest concentrations, and is like the Nanjemoy in that 

it has a high land area to water area ratio.

• Scores for indicator bacteria levels in 2010 and 2011 were somewhat higher than other years 

for most rivers (Figure WQ23).
34

Living aquatic resources are organisms that possess an ecological, commercial, or social value. In 

the Chesapeake Bay, many species of fish and shellfish represent important living resources as 

they constitute a valuable component of commercial and recreational economies. In Maryland 

in 2012, over 33,000 metric tons of fish and shellfish were caught commercially, and the combination 

of both commercial and recreational fishing generated over $1 billion [3]. The availability of these 

important resources in the Chesapeake Bay is predicated on the amount of healthy habitat that supports 

their reproduction, growth, and survival. Stressors, such as pollution and habitat loss, can induce 

drastic changes in the size and health of populations of living resources [62]. As discussed in the water 

quality chapter, these stressors may be related to land alterations and other human activities. Therefore, 

measuring living resource population sizes and determining the overall health of these populations 

allows us to evaluate the relative health of estuarine habitats in relation to land use. Assessing the health 

of living resources allows for a more direct measure of the combined effects of these stressors and of 

ecological change than do individual water quality or habitat variables.

Responses to environmental stressors by living organisms can occur at all levels of biological 

organization. For example, intermittent stressors can cause changes in gene expression, resulting in 

altered physiological conditions. If a stressor persists, the structure and function of internal organs can 

be affected. Often, organismal responses to environmental stressors can be observed before there are 

consequences on the population level, particularly if the stress impacts the reproductive success of the 

organisms. In this way, living resources provide an early warning of alterations to their environment. 

Finally, chronic or prolonged habitat degradation or stress can lead to broad scale changes in fish and 

shellfish populations.

In this study, living resources were used as bioindicators of estuarine health. Responses at each level 

of biological organization were measured in this study to create a holistic picture of the health of each 

river. Species studied for sub-lethal health impacts included white perch (Morone americana) and the blue 

crab (Callinectes sapidus). Assessments of fish populations and communities were conducted in nearshore 

and mid-river habitats by identifying and counting all species of fish captured in trawl and seine nets.

Chesapeake Bay Ecosystem Assessment Living Resources

Image LR1: A NOAA scientist from the Cooperative Oxford Laboratory pulls a seine net.
35

Crab Host Response and 

Parasites

The blue crab, Callinectes sapidus (Image LR2), 

is a key component of the Chesapeake Bay 

ecosystem. A bottom-feeder, it preys on a 

wide range of invertebrates and is a major 

food source for many fish species [63]. Its 

consumption of various bivalve species may 

have an effect on the composition of softbottom communities [64]. Furthermore, the 

blue crab has been found to possess several 

quantifiable characteristics that act as indicators 

of environmental change.

Blue crab characteristics measured for this 

study fall under the two categories of host 

response and parasitology. Host response 

refers to physical signs of an organism’s 

reaction to some stressor. Blue crab stressors 

include disease and abnormal environmental 

parameters. Host responses in C. sapidus

include inflammation, nodule formation 

and tissue necrosis [63]. It is often difficult 

to tell what type of stressor caused a given 

host response. However, unlike disease and 

environmental parameters, parasites are often 

easier to see, if present in sufficient numbers. 

Therefore, parasitology was further studied, 

and parasites including ciliates, larval worms, 

microsporidians, gregarines and viruses were 

observed. Ciliates feed on bacteria, so higher 

numbers of ciliates on crab gills may indicate 

higher nutrient levels in the water, and therefore 

lower water quality. Furthermore, if ciliates are 

dense enough on crab gills they may inhibit 

respiration, which along with low levels of 

dissolved oxygen may lead to anoxia.

Figure LR1: Percent of crabs from each river showing a host 

response (top) and with parasites (bottom). No significant 

differences were detected for host response.

Background

Methods

Thirty or more crabs from each watershed were 

collected using a baited line laid along the river 

bottom. Crabs were then chilled to reduce mobility. 

Within a few hours, tissues were dissected and 

preserved for routine histopathological examination 

using light microscopy [65]. Crabs were assessed 

for any host responses and any parasites. Rivers 

were ranked by prevalence of host response and 

prevalence of parasites.

Chesapeake Bay Ecosystem Assessment Living Resources

Image LR2 (Right): A NOAA scientist from the 

Cooperative Oxford Lab holds a blue crab prior to 

dissection.

0

20

40

60

80

100

Corsica Sassafras Magothy Middle Rhode Nanjemoy

Percent of Crabs Affected

River

Crabs with Parasites

A,C A B,C,D A,D C A,C

0

20

40

60

80

100

Corsica Sassafras Magothy Middle Rhode Nanjemoy

Percent of Crabs Affected

River

Host Response in Blue Crabs
36

Results

Figure LR4: Overall host response score for each river. Error bars represent one standard deviation.

Score Criteria for Crab Host Response and Parasitology

Score 1 2 3 4 5

Criteria (% prevalence of any host response) 100 75 50 25 0

Criteria (% prevalence of any parasite) 100 75 50 25 0

Figure LR2: Scaling from percentage to score for crab host response and parasitology.

Figure LR3: Host response scores by river and year.

River

Corsica

Sassafras

Middle

Magothy

Rhode

Nanjemoy

Mi

Ma

C

R

S

N

Abbr 2007 2008 2009 2010 2011 2012

1 s 2 s 3 s 4 s 5 

S

C

Ma

Mi

R

N

Chesapeake Bay Ecosystem Assessment Living Resources

Crab Host Response Findings

• The percent of crabs with host response was not statistically different between any of the 

rivers (Figure LR1).

• However, for rivers with similar salinity ranges (Figure W5), scores for host response were 

poorer in agricultural rivers (Corsica and Sassafras) and better in urban rivers (Magothy and 

Middle) (Figure LR4), which is similar to the nutrient results.

• Host response scores were generally better than parasite scores.
37

Results Continued

Figure LR6: Overall crab parasite scores by river. Error bars represent one standard deviation.

Figure LR5: Heat map of crab parasite scores by river and year.

River

Corsica

Sassafras

Middle

Magothy

Rhode

Nanjemoy

Mi

Ma

C

R

S

N

Abbr 2007 2008 2009 2010 2011 2012

1 s 2 s 3 s 4 s 5 

S

C

Ma

Mi

R

N

Chesapeake Bay Ecosystem Assessment Living Resources

Crab Parasite Findings

• There was higher prevalence of parasites in crabs from the higher salinity rivers (Corsica, 

Magothy, and Rhode) (Figure LR1).

• In contrast to host response, scores for the prevalence of crabs with parasites were best in the 

agricultural rivers (Corsica and Sassafras) and worst in the forested/mixed-use rivers (Rhode 

and Nanjemoy), within salinity group (Figure LR6).

• There was notable interannual variation in all rivers except the Corsica (Figure LR5).
38

Fish Abundance

Abundance is a measure of the relative 

proportions of a given group of species in a given 

environment [66]. The abundance and diversity of 

the finfish community are indicators of the overall 

suitability of the aquatic ecosystem to support 

growth. Appropriate physical habitat, acceptable 

water quality, proximity to spawning grounds, 

and sufficient food availability all play a role in 

determining the types and numbers of fish a water 

body can support [67-68].

Estuarine systems are highly variable in nature with annual changes in salinity structure, bay grasses, and 

recruitment success. Because of this variability, fish which inhabit estuarine systems tend to be tolerant 

to change and assessing trends in abundance should be conducted over several years to address the 

impact of annual cycles on recruitment. It 

is also necessary to characterize both fish 

inhabiting open water and those staying near 

to shore in the system.

Background

Methods

Figure LR7: Fish abundance in each river per trawl (top) and seine 

(bottom).

Chesapeake Bay Ecosystem Assessment Living Resources

Image LR3: NOAA scientists from the Cooperative 

Oxford Lab pull in a seine net.

A 100 foot beach seine and 16 foot otter 

trawl were used to sample sites throughout 

each river six times per year. Seines and 

trawls were deployed in a standardized 

manner and the number of individuals 

collected for each fish species was tallied. 

Because no criteria exists for fish abundance, 

we scored individual abundance values based 

on where they fell within the range of all 

observed values. First, all abundance values 

were ranked and quantiles were calculated. 

Samples were then scored by comparison 

to the quantiles, as shown in Figure LR9. 

Furthermore, data for fish abundance 

collected by seine in near shore shallow 

waters was separated from fish abundance 

collected by trawl in mid-river deep water, in 

order to look at differences between these 

habitats.

0

100

200

300

400

500

600

700

Corsica Sassafras Magothy Middle Rhode Nanjemoy

Number of Fish

River

Fish Abundance per Trawl

A A,D B A,D C D

0

100

200

300

400

500

600

Corsica Sassafras Magothy Middle Rhode Nanjemoy

Number of Fish

River

Fish Abundance per Seine

A,B A A B A A
39

Figure LR8: Relative abundance of the five most abundant species in each river, in addition to the total relative 

abundance of all other species.

Chesapeake Bay Ecosystem Assessment Living Resources

53%

15%

8%

8%

5%

11% Corsica

White Perch

Atlantic Menhaden

Atlantic Silverside

Spot

Mummichog

Other (43 Species) 71%

6%

4%

3%

3%

13% Sassafras

White Perch

Gizzard Shad

Spot

Spottail Shiner

Brown Bullhead

Other (32 Species)

30%

15%

12%

11%

7%

25%

Magothy

White Perch

Atlantic Silverside

Atlantic Menhaden

Spot

Bay Anchovy

Other (42 Species)

52%

18%

8%

7%

3%

12% Middle

White Perch

Gizzard Shad

Bay Anchovy

Pumpkin Seed

Blueback Herring

Other (33 Species)

18%

18%

18%

18%

12%

16%

Rhode

Atlantic Silverside

Bay Anchovy

Atlantic Menhaden

Spot

White Perch

Other (47 Species)

74%

8%

3%

2%

2%

11% Nanjemoy

White Perch

Bay Anchovy

Gizzard Shad

Blueback Herring

Spot

Other (35 Species)
40

Results

Score Criteria for Fish Abundance

Abundance Data Quartiles 0-20% 21-40% 41-60% 61-80% 81-100%

Index Score 1 2 3 4 5

Figure LR9: Explanation of fish abundance scoring criteria.

Fish Seine Abundance Findings

• The mixed-use Rhode River had the most balanced distribution of fish species, while most 

other rivers were dominated by white perch (Figure LR8).

• Nearshore abundance was greatest in the urban Middle and agricultural Corsica Rivers, but 

overall, most systems were similar. 

• No correlations were observed with water quality or watershed land use patterns.

Figure LR11: Overall fish abundance scores from near shore (seine) by river. Error bars represent one standard 

deviation.

Figure LR10: Heat map of fish abundance scores from near shore (seine) by river and year.

1 s 2 s 3 s 4 s 5 

S

C

Ma

Mi

R

N

Chesapeake Bay Ecosystem Assessment Living Resources

River

Corsica

Sassafras

Middle

Magothy

Rhode

Nanjemoy

Mi

Ma

C

R

S

N

Abbr 2007 2008 2009 2010 2011 2012
41

Results Continued

Fish Trawl Abundance Findings

• There was no general trend in trawl abundance related to land use type (Figure LR7). 

• The urban Magothy, with the lowest dissolved oxygen concentrations, had lowest fish 

abundance (Figure LR7).

• The Nanjemoy, Middle, and Corsica and Sassafras Rivers generally had higher mid-river 

abundance than the Magothy and Rhode (Figure LR7). 

• The overall catch in all systems, except for the Rhode and Magothy, was dominated by white 

perch (>50%).

• The Magothy and Rhode were also slightly higher in salinity, lower in nutrients and turbidity, 

and more distant from major white perch spawning areas.

Figure LR13: Overall fish abundance scores from mid-river (trawl) by year. Error bars represent one standard 

deviation.

Figure LR12: Heat map of fish abundance scores from mid-river (trawl) scores by river and year.

1 s 2 s 3 s 4 s 5 

S

C

Ma

Mi

R

N

River

Corsica

Sassafras

Middle

Magothy

Rhode

Nanjemoy

Mi

Ma

C

R

S

N

Abbr 2007 2008 2009 2010 2011 2012

Chesapeake Bay Ecosystem Assessment Living Resources
42

Fish Body Fat Index

Fish health is often assessed by observing 

average condition, or overall well-being, of 

a population. These observations regularly 

use metrics of fish nutritional status. 

Healthy ecosystems possess adequate 

amounts of forage for fish populations 

to not only survive, but for individuals 

to grow and reproduce. Stressors that 

interrupt the ability of fish to obtain 

forage reduce individuals’ nutritional status. 

In addition, some stressors may significantly alter the biochemical patterns that govern metabolism [69]. 

In this study, fish muscle tissue moisture and the presence of body fat were examined. During periods 

of starvation, moisture levels in fish increase as lipid reserves are reduced. Well-fed fish accumulate fat 

reserves in their abdominal cavity. The presence and quantity of these reserves, as measured by the body 

fat index (BFI), provides a rapid method of determining relative nutritional status. The relationship 

between BFI and measurements of both tissue lipid and tissue moisture were verified in this study (see 

Figure LR15) and as well as in previous research [70]. During this assessment, BFI was examined in 

white perch collected in all six years while tissue moisture levels were analyzed for three years of the 

study to verify the efficacy of the index. This approach assumed that a majority of fish collected in rivers 

with healthy habitat would possess abundant fat reserves relative to rivers with poor habitat quality.

Figure LR14: Average fish body fat index values for each river.

Background

Methods

Fat content in the body cavities of white perch was assigned a semi-quantitative score from 0 to 3 based 

on visual observation. Fish tissue moisture was determined by weighing samples of white perch muscle 

tissue before and after oven-drying the tissue. 

Moisture was then calculated as a percent 

of the total weight of the fish based on the 

percent of its total weight in the sample.

Tissue moisture and body fat were then 

compared using an analysis of variance, and 

found to correlate significantly (Figure LR15). 

Body fat scores were translated to index 

scores from 1-5 by a scaling equation, such 

that a BFI score of 0 is equivalent to an index 

score of 1, and a BFI score of 3 is equivalent 

to an index score of 5 (Figure LR16).

Figure LR15: This table shows that average moisture content 

for fish in each BFI category is significantly different from all the 

other BFI categories.

Chesapeake Bay Ecosystem Assessment Living Resources

0

0.5

1

1.5

2

2.5

3

Average Fish Body Fat Index (0

Corsica Sassafras Magothy Middle Rhode Nanjemoy

-3)

River

Average Fish Body Fat Index

A B A,B A,B C A

76

77

78

79

80

81

82

0 1 2 3

Tissue Mouisture (%)

BFI Category

Moisture Content of BFI Categories

A B C D
43

Results

Score Criteria for Body Fat Index

Body Fat Score 0 1.5 3

Index Score 1 3 5

Figure LR16: Equating body fat scores to corresponding index scores.

Figure LR18: Overall body fat index scores by river. Error bars represent one standard deviation.

1 s 2 s 3 s 4 s 5 

Figure LR17: Heat map of body fat index scores by river and year.

C

S

Ma

Mi

R

N

Body Fat Index Findings

• Fish from the mixed land use Rhode River had significantly more body fat than fish from all 

other rivers (Figure LR14).

• Differences in BFI score did not clearly separate the rivers.

• BFI scores from the rivers tended to improve over time (Figure LR17).

River

Corsica

Sassafras

Middle

Magothy

Rhode

Nanjemoy

Mi

Ma

C

R

S

N

Abbr 2007 2008 2009 2010 2011 2012

Chesapeake Bay Ecosystem Assessment Living Resources
44

External Fish Parasites

Fish parasites tend to be found on 

gills, intestines and skin. Research 

has shown that the abundance of 

fish parasites, particularly external 

parasites, are indicators of fish 

health in relation to river condition 

[71]. Environmental conditions 

such as poor water quality and high 

contaminant loads correspond 

to higher parasite quantities [71]. 

From an organismal perspective, 

poor fish condition and abundant 

intermediate parasite hosts (generally benthic macroinvertebrates) also relate to higher parasite loads.

For this study, external parasites were counted on white perch, as these fish are found in each of 

the rivers, and they tend to spend most of their adult life within an individual river [72]. The most 

common parasites found on white perch in the six Chesapeake Bay rivers in this study included ciliated 

protozoans, encysted flatworms, and gill flukes, which were found on the gill tissues and/or the mucous 

which covers the skin. Less commonly, copepod and isopod parasites were found attached to the gills 

and fins.

Figure LR19: Percent of fish with parasites from each river.

Background

Methods

At least 12 white perch were collected 

from three different locations within 

each river during the fall of each year.

In the field, small sections of gills and 

samples of the mucous scraped from 

the skin were taken from fish collected 

by various means (trawl, beach seine, 

hook and line). External parasites were 

counted. The intensity, or number of 

external parasites counted, was converted 

into a score, representing an index of 

external parasite burden.

Image LR4: Image of an isopod parasite on the gills of a white perch. 

Photo courtesy of M. Matsche, MDDNR.

Chesapeake Bay Ecosystem Assessment Living Resources

0

20

40

60

80

100

Corsica Sassafras Magothy Middle Rhode Nanjemoy

Percent of Fish

River

Percent of Fish with Parasites

A A B A C A
45

Results

Score Criteria for External Fish Parasites

Number of parasites per section >3 1-3 <1

Index Score 1 3 5

Figure LR20: Translation from parasite density to index score.

Figure LR22: Overall external fish parasite scores by river. Error bars represent one standard deviation.

1 s 2 s 3 s 4 s 5 

Figure LR21: Heat map of external fish parasite scores by river and year.

S

C

Ma

Mi

R

N

External Fish Parasite Findings

• Fish from the two agricultural systems (Corsica and Sassafras) consistently possessed relatively 

high parasite loads (Figure LR19).

• Across all rivers, fish collected in 2011 possessed higher parasite loads and corresponding low 

scores (Figure LR21), indicating a possible overarching ecological impact independent of land 

use type.

• Relative scores between the two urban systems, the Magothy and Middle, and the two forest 

and mixed-use systems, the Rhode and Nanjemoy, failed to demonstrate a consistent pattern 

of parasite abundance that could be linked to land use.

River

Corsica

Sassafras

Middle

Magothy

Rhode

Nanjemoy

Mi

Ma

C

R

S

N

Abbr 2007 2008 2009 2010 2011 2012

Chesapeake Bay Ecosystem Assessment Living Resources
46

Fish Macrophage 

Aggregates

Macrophage aggregates are accumulations 

of white blood cells involved in the 

capture, transport, and destruction of 

foreign materials, such as contaminants, 

heavy metals, parasites and dead cells. 

These cells clump together in focal 

centers to destroy foreign materials 

and reclaim useful tissues and cells. 

Macrophage aggregates can be detected 

using histological techniques, where fish 

tissue is stained, preserved in wax, sliced 

into very thin layers and examined under 

a microscope. The size and density of 

macrophage aggregates in the spleens of 

fish are known to be indicators of impaired water quality. By looking at nearly a thousand fish collected 

from many estuaries around the US, criteria have been developed to use macrophages as indicators of 

fish health [73]. Specifically, macrophage groupings larger than 5.0x10-5 mm2 are considered aggregates. 

If aggregates at or above this size are observed at a density below 15 per mm2 of fish tissue, the system 

is scored as healthy. If aggregates are observed at a density above 40 per mm2, the system is considered 

impaired. Densities between 15 and 40 per mm2 indicate intermediate river health [73].

Image LR5: A 10x magnified image of macrophage aggregates 

(stained dark blue) from a white perch spleen tissue sample.

Background

Methods

White perch spleens were 

embedded in paraffin, cut to 

5 microns, and stained using 

either Mayer’s hematoxylineosin-phloxine or Perl’s Prussian 

Blue [65]. The stained tissue 

was examined using a Nikon 

Coolscope, in conjunction with 

the freeware ImageJ program. 

Macrophages larger than 5.0x10-6

mm2 were counted from randomly 

selected areas on each slide. The 

densities of these were then 

calculated per mm2

of fish tissue. 

Scores were assigned according to 

Figure LR24. Figure LR23: Average macrophage aggregate densities in each river.

Chesapeake Bay Ecosystem Assessment Living Resources

0

10

20

30

40

50

60

70

Number of Macrophage Aggregates 

Corsica Sassafras Magothy Middle Rhode Nanjemoy

per mm2

River

Macrophage Aggregates

A B C D E B
47

Results

Score Criteria for Macrophage Aggregates

Density (Macrophage Aggregates

per mm2 of tissue) >40 15-40 <15

Index Score 1 3 5

Figure LR24: Macrophage aggregate density thresholds and their corresponding index scores.

Figure LR26: Overall macrophage aggregate scores by river. Error bars represent one standard deviation.

1 s 2 s 3 s 4 s 5 

Figure LR25: Heat map of macrophage aggregate scores by river and year.

S

C

Ma

Mi

R

N

Fish Macrophage Aggregate Findings

• Lower salinity rivers (Sassafras, Middle, and Nanjemoy) had more macrophage aggregates per 

area of tissue than the higher salinity river (Corsica, Magothy, and Rhode) (Figure LR23).

• There was a high degree of interannual variability, particularly in the latter years of the study.

• Most systems had high levels of macrophage aggregates in 2010 and low levels in 2011 

(Figure LR25).

River

Corsica

Sassafras

Middle

Magothy

Rhode

Nanjemoy

Mi

Ma

C

R

S

N

Abbr 2007 2008 2009 2010 2011 2012

Chesapeake Bay Ecosystem Assessment Living Resources
48

Fish Disease

Disease prevalence in fish and 

other aquatic organisms has 

been linked to river health. For 

disease to progress in a natural 

fish population, three ingredients 

must be present: a susceptible fish 

population, a viable pathogen, 

and environmental stress. In 

theory, environmental conditions 

that are stressful to organisms or 

beneficial to pathogens can lead 

to increased incidence of disease. Evidence for a relationship between environmental stress and fish 

disease has been accumulating for decades [74]. Recently a link between poor water quality and a higher 

incidence in disease has been developed for Chesapeake Bay fish (Mark Matsche, MD DNR, personal 

communication).

In this study, mycobacteriosis prevalence in white perch was analyzed as an indicator of environmental 

health. Mycobacteriosis is a disease caused by several species of the genus Mycobacterium. Immune 

response to mycobacterial infections include inflammation and granuloma formation in the spleen 

[75]. Inflammation diverts greater blood flow to the infected area to deliver disease-fighting cells, and 

granulomas are capsules which form around the infected area to contain it. 

Figure LR27: Percent of fish with spleenic inflammation due to disease or a 

combination of disease and internal parasites.

Background

Methods

White perch were necropsied with 

organs processed for histopathology, 

and pathological changes were noted. 

Mycobacteriosis presence was judged by 

the inflammation in the spleen (exclusive 

of inflammation caused solely by parasites) 

and the presence of acid-fast bacteria 

(bacteria such as Mycobacterium that have 

thick, waxy outer membranes). The percent 

of fish showing these disease conditions 

is shown in Figure LR27. The severity of 

splenic inflammation for each fish was rated 

as severe, moderate, or none (normal). 

These ratings were then converted to scores 

Image LR6: A NOAA scientist prepares a white perch for necropsy. as shown in Figure LR28.

Chesapeake Bay Ecosystem Assessment Living Resources

0

10

20

30

40

50

60

Corsica Sassafras Magothy Middle Rhode Nanjemoy

Percent of Fish with Spleenic 

Inflammation

River

Fish Disease

A B B B B B
49

Results

Score Criteria for Fish Disease

Degree of Tissue Inflammation Severe Moderate None (Normal Tissue)

Index Score 1 3 5

Figure LR28: Translation of tissue inflammation assessment to index score.

Figure LR30: Overall fish disease scores by river. Error bars represent one standard deviation.

1 s 2 s 3 s 4 s 5 

Figure LR29: Heat map of fish disease scores by river and year.

S

C

Ma

Mi

R

N

Fish Disease Findings

• Corsica River fish had much higher disease prevalence than all other systems (Figure LR27).

• Disease prevalence followed general land use categorization with agricultural systems having 

higher prevalence than the others (Figure LR27).

• Disease severity was also highest in the Corsica, but did not follow the same pattern as 

prevalence, with diseased fish in the Nanjemoy and Middle having more severe inflammation 

than Sassafras, Magothy, and Rhode River fish (Figure LR30). 

River

Corsica

Sassafras

Middle

Magothy

Rhode

Nanjemoy

Mi

Ma

C

R

S

N

Abbr 2007 2008 2009 2010 2011 2012

Chesapeake Bay Ecosystem Assessment Living Resources
50

Submerged Aquatic 

Vegetation

Submerged aquatic vegetation 

(SAV) in the Chesapeake Bay 

includes several species of bay 

grasses that grow underwater in 

the shallow areas of the Bay and 

its tributaries. SAV is both an 

excellent indicator and mediator 

of Bay health. As an indicator, 

SAV acreage declines steeply in 

response to increases in pollution, 

but respond well to improvements 

in water quality. Furthermore, since 

SAV relies on photosynthesis and therefore requires sunlight, its ability to thrive is closely linked to water 

clarity. As a mediator, SAV improves water quality, including clarity, by filtering out pollutants, trapping 

suspended sediments, and oxygenating the water [76]. Historically, all six rivers have supported SAV beds, 

occasionally in greater extent than during our study, though the amount of SAV has varied considerably 

over time [77,78].

Figure AV1: Percent of river area covered by SAV.

0

5

10

15

20

Corsica Sassafras Magothy Middle Rhode Nanjemoy

Percent of River Area

River

Submerged Aquatic Vegetation

Background

Methods

Unlike the other variables in this study, data obtained from the Virginia Institute of Marine Science [77] 

was used to determine the area in each of the six studied rivers that was covered by SAV beds from 2007 

to 2012. This area was then divided by the total area of each river to find a percent coverage for each 

river, each year. .

The Chesapeake Bay Program (CBP) has established a restoration goal of 185,000 total acres of SAV 

in the Bay. This goal was divided into several 

categories, depending on the salinity regime 

of the location [79]. The rivers in this study 

fell into either the low salinity (oligohaline) or 

moderate salinity (mesohaline) categories for 

CBP goals, which were 10,334 and 120,306 

acres, respectively. The total oligohaline 

and total mesohaline surface areas of the 

Bay were divided by these values to come 

up with goal percent coverage values [80]. 

The mesohaline goal was 6.45% and the 

oligohaline goal was 4.39%. For this study, the 

ranges from 0 to 6.45% and 0 to 4.39% were 

then scaled to a score from 1 to 5, where any 

river in the appropriate salinity regime with 

greater than 6.45% or 4.39% coverage was 

scored a 5 (see Figure AV2).

Image AV1: SAV beds in the Choptank River, pictured from below 

(left) and above (right) the surface. Images courtesy of Ben Fertig, 

Integration and Application Network, University of Maryland 

Center for Environmental Science (ian.umces.edu/imagelibrary/).

Chesapeake Bay Ecosystem Assessment Aquatic Vegetation
51

Results

Score Criteria for Submerged Aquatic Vegetation

Mesohaline River Coverage (%) 0 3.23 >6.45

Oligohaline River Coverage (%) 0 2.20 >4.39

Index Score 1 3 5

Figure AV2: Scaling from percent SAV coverage to score, dependent on salinity profile.

Figure AV4: Overall SAV scores by river. Error bars represent one standard deviation.

1 s 2 s 3 s 4 s 5 

Figure AV3: Heat map of SAV scores by river and year.

C

S

Ma

Mi

R

N

Submerged Aquatic Vegetation Findings

• The rivers diverged by salinity profile, perhaps due to the success of Widegeon grass and 

other low salinity (oligohaline) species [42].

• The Magothy had more SAV than the other moderate (mesohaline) salinity rivers (Corsica and 

Rhode), corresponding to its better water clarity.

• The Nanjemoy had less SAV than the other low salinity (oligohaline) rivers (Sassafras and 

Middle) corresponding to its poor water clarity.

River

Corsica

Sassafras

Middle

Magothy

Rhode

Nanjemoy

Mi

Ma

C

R

S

N

Abbr 2007 2008 2009 2010 2011 2012

Chesapeake Bay Ecosystem Assessment Aquatic Vegetation
52

This study assessed ecological conditions in six rivers of the Chesapeake Bay watershed and related differences in those conditions to potential stressors, primarily those resulting from land use 

activities. The assessment uncovered a mix of expected relationships and some surprising trends. 

Major suspected findings include high nutrient concentrations and cloudy waters in the agricultural 

rivers, abundant but unhealthy fish in the agricultural rivers, and relatively balanced nutrient levels and 

healthier fish in the mixed-use and forested rivers. The unexpected outcomes include mixed signals in the 

urbanized rivers for water quality and living resources, multiple signs of poor health in the forested river, 

the nearly complete lack of SAV in the mesohaline rivers, and multiple instances of strong interannual 

variability across all studied rivers without a clear correlation to changing weather patterns.

The traditional agricultural signals of high nutrient and chlorophyll a concentrations were considerably 

stronger in the two agriculturally dominated watersheds, the Corsica and Sassafras, than the two 

urban systems, the Magothy and Middle. This finding suggests that controls on urban point sources 

of nutrients, such as wastewater treatment plants and industrial effluents, have been more effective in 

reducing nutrient inputs then those for nonpoint sources, such as runoff from agricultural fields. As 

expected for the nutrient-enriched agricultural watersheds, high chlorophyll a was correlated to relatively 

low Secchi depths and sparse SAV. This set of conditions can occur when excessive phytoplankton 

growth clouds the water column and prevents sunlight from penetrating to the bottom where SAV 

grows. 

Although high nutrient and phytoplankton concentrations often lead to low dissolved oxygen in 

summertime, when waters become vertically stratified, dissolved oxygen concentrations in the two 

agricultural systems were sufficient to support living resources. In fact, open water fish abundances were 

as high or higher in the agriculturally dominated watersheds than in all other systems except the forestlined Nanjemoy River. High levels of nutrients and phytoplankton in the Corsica and Sassafras appear to 

be consumed rapidly and help support the relatively abundant fish populations found there.

Chesapeake Bay Ecosystem Assessment Synthesis

Image S1: Floating vegetation on the Sassafras River.
53

Fish disease was common in white perch from both 

agricultural rivers. In the Corsica, 43% of fish were 

affected by disease, nearly twice the proportion of the next 

most affected river, the Sassafras. Fish disease prevalence 

was lower in the urbanized and mixed-use rivers and 

lowest in the and forested rivers. Disease severity (as 

measured by the stage of advancement of infections) in 

fish from the Corsica was also high, though the Sassafras 

did not show high severity. Disease prevalence and 

severity in the agricultural rivers may, in part, be the result 

of stressful competition for resources among the large 

open-water fish populations in those rivers; however, high 

abundances and good health in other rivers suggest this 

may not be the only factor.

 

Conditions in the highly urbanized Middle and Magothy 

rivers were mixed. Although nutrient concentrations 

were lower than the agricultural systems, values were 

still excessive compared to established criteria. Secchi 

depth scores were best in the Magothy and Middle 

when compared to the other rivers in their respective 

salinity groups. Dissolved oxygen in bottom waters of 

the Magothy was lower than all other rivers, though this 

trend was not severe enough to be reflected in the overall 

dissolved oxygen scores for that river. The Magothy also 

had the lowest fish abundance scores for the mid-channel 

habitat (trawl samples), perhaps related to the relatively low oxygen levels in the bottom waters. In 

contrast, the Middle River had relatively high abundances of fish in both the open water trawl samples 

and the nearshore seine samples. Both urbanized rivers may have been expected to show low abundance 

due to the effects of urban pollutants like heavy metals and PCBs. Mixed abundance scores suggest that 

urban pollution may not be the defining factor. The Middle River also had relatively low fish diversity, 

though the diversity of fish in this system, as well as the other two low salinity rivers (Nanjemoy and 

Sassafras), may be related in part to the high numbers of white perch and the proximity of the rivers to 

white perch spawning grounds. In a previous report on the first three years of this study (2007 to 2009), 

levels of chemical contaminants and toxic sediments were higher in the urbanized Magothy than in the 

Corsica and Rhode [7]. Unfortunately, benthic contaminant information was not collected from the 

other three rivers.

The Rhode River, which is partially forested with low to moderate urbanized areas, and the Nanjemoy, 

which is largely forested, had complex condition signatures as well. Both rivers tended to have lower 

nitrogen and chlorophyll a concentrations, and lower fish disease than the two agricultural rivers. 

Nutrient loads in these rivers were expected to be low because forested land is effective at trapping 

runoff in the dense network of tree roots that permeate the soil. Furthermore, more undisturbed land 

was expected to correlate to healthier individual fish, because forested lands leach much less pollutants 

into the water body than urban or agricultural lands.

Chesapeake Bay Ecosystem Assessment Synthesis

Image S2: A great blue heron stands beside the 

Tred Avon River. Image courtesy of Jane Hawkey, 

Integration and Application Network, University of 

Maryland Center for Environmental Science (ian.

umces.edu/imagelibrary/).
54

Although the relatively high incidence of fish disease seen in the agricultural systems may be related to 

high densities of individuals living in close proximity and the associated stress, the Nanjemoy had the 

highest fish densities of all rivers, but also the lowest disease incidence. The Rhode was also the most 

balanced river in terms of fish diversity and the Nanjemoy averaged more than five times the number 

of fish captured per trawl than the Magothy. However, the Rhode and Nanjemoy both had conditions 

that indicated some stress. For example, both rivers suffered from poor water clarity, with the Nanjemoy 

having the worst water clarity of all rivers. The prevalence of crab parasites was also higher in the Rhode 

and Nanjemoy, when compared to the urban and agricultural rivers of similar salinity. While the presence 

of fish parasites was high in the Nanjemoy, fish from the Rhode had much lower incidence of parasites.

An interesting interplay between water clarity and nutrient concentrations emerged that helped to 

contrast conditions in the two relatively undeveloped rivers, the Rhode and Nanjemoy. These two rivers 

had poor water clarity, but perhaps for slightly different reasons. Indicator bacteria and phosphorus 

concentrations were very high in the Nanjemoy, while chlorophyll a concentrations were relatively low. 

Because phosphorus and indicator bacteria tend to bind to sediments, suspended sediments likely played 

a significant role in the poor water clarity there. While sediments also likely played a role in Rhode River 

water clarity, and the influx of large amounts of sediment from the heavily forested headwater area 

of the watershed has been noted [81], the high level of chlorophyll a in the Rhode suggests a more 

important role for phytoplankton in water clarity conditions there. The unexpected presence of elevated 

suspended sediment concentrations in the two forested watersheds may be related to resuspension of 

sediments from subtidal mud flats [81].

In addition to land use, a major factor separating the six rivers was salinity. In anticipation of this, two 

sets of three rivers were selected during the study design to represent mesohaline rivers (Corsica, Rhode, 

and Magothy; sampled 2007-2011) and oligohaline rivers (Nanjemoy, Middle, and Sassafras; sampled 

2010-2012). For chlorophyll a, Secchi depth, and submerged aquatic vegetation (SAV), the index criteria 

used to assess condition depended on salinity. This was most apparent for SAV, where the goals for 

restoring SAV beds are greater in moderately saline areas than in low salinity regions. Additionally, the 

three low salinity rivers had higher fish abundances in both the nearshore (seine) and mid-river (trawl) 

habitats, likely due to the predominance of white perch and their recruitment from nearby freshwater 

spawning grounds.

Chesapeake Bay Ecosystem Assessment Synthesis

Image S3: NOAA scientists from the Cooperative Oxford Laboratory photographed this small boat while conducting a 

sampling mission.
55

Chesapeake Bay Ecosystem Assessment Synthesis

Although a number of the variables showed interannual variability, only a few varied the same way across 

all six rivers. Chlorophyll a scores tended to degrade from 2007 to 2012 for all rivers. In contrast, index 

scores for crab host response and fish macrophage aggregates had notable interannual variability for all 

rivers that did not follow a sustained chronologic trend. Macrophage aggregate scores were particularly 

variable in the last three years of the study, making it the only factor that had considerably more variation 

between years than between rivers. For macrophage aggregates, most systems had elevated levels in 2010, 

and very low levels in 2011. However, systems with greater white perch abundance tended to have lower 

index scores than those with smaller perch populations. In addition to abundance, elevated macrophage 

aggregates also correlated with elevated indicator bacteria and higher turbidity in the water, and higher 

air temperature. 

Several management implications can be drawn from this study. Primary among them is the need for 

managers to persist in current efforts to reduce non-point introduction of nitrogen, phosphorus and 

sediments to Chesapeake Bay tributaries. This particularly applies to the urbanized Magothy River and 

the heavily forested Nanjemoy where suspended sediments contribute to water quality issues. Another 

management implication is the need to preserve habitat to support diverse and healthy fish populations, 

particularly in spawning areas of the Bay. Our findings suggest that abundances and health of fish may 

involve trade-offs, with highly eutrophied systems supporting moderate to large numbers of fish, but in 

poorer health. A third implication is that there remains a need to better assess the impact of crab health 

on population sizes for setting appropriate harvest limits.

Study Conclusions

• All rivers showed some signs of stress with the Rhode River being least impacted overall.

• The strongest signals in this study were detected for excessive nutrients and phytoplankton in 

watersheds with predominant agricultural uses.

• The strongest organismal indicator was for lower fish disease prevalence in the heavily 

forested Nanjemoy watershed

• Urban rivers had good water clarity and healthy fish, but excess nutrients and low dissolved 

oxygen were observed in bottom waters in the relatively deep Magothy River.

• No strong chronological trends were detected but there were some weak correlations 

between air temperatures and both fish abundance and the intensity of macrophage 

aggregates in fish tissues.

• Fish health was inversely related to nutrients, phytoplankton, and fish abundance.

• Crab health results were mixed with heaviest parasite incidence in low development areas and 

lowest host response incidence in high development areas.

• Rivers in different salinity zones seem to behave differently for a number of variables, 

especially for submerged aquatic vegetation and fish abundance.
56

Chesapeake Bay Ecosystem Assessment Partners

The following individuals provided integral support for this endeavor:

Ana Baya, Bob Bingaman, Sarah Bornhoeft, Juli Brush, Rebecca Burton, Captian Skip Collier, 

Jimmy Councilman, Blair DeLean, Steve Early, AJ Fry, Dorothy Howard, Lois Lane, Jay Lewis, Rudy 

Lukacovic, Meg Maddox, Laura Marson, Margaret McGinty, Maggie Miller, Jen O’Keefe, Chris Ottinger, 

Matt Rhodes, Laura Robertson, Kristi Shaw, Suzanne Skelley, Cindy Stine, Crystal Thomas, Sue Tyler, 

Jim Uphoff, Bob Wood.

The following individuals also lent an invaluable helping hand:

Pam Baker, David Bruce, Ron Cheezum, Tracy Gill, Steve Giordano, Mejs Hasan, LeeAnn Hutchison, 

Hannah Martin, Ed Martino, Mark Matsche, Bart Merrick, Kevin Rosemary, Howard Townsend, and 

Butch Webb.

Thank You to Our Partners

The Cooperative Oxford Laboratory is indebted to:

NOAA Chesapeake Bay Office

Maryland Department of Natural Resources

Maryland Department of Agriculture

University of Maryland

Organizations

Individuals

Image P1: Rain did not deter field sampling.
57

Chesapeake Bay Ecosystem Assessment References

1. Chesapeake Bay Foundation. “Captain John Smith.” <http://www.chesapeakebay.net/discover/

bayhistory/johnsmith> Accessed 07/24/2015.

2. Chesapeake Bay Program. “Population Growth.” <http://www.chesapeakebay.net/issues/issue/

population_growth#inline> Accessed 07/27/2015.

3. National Marine Fisheries Service. 2014. Fisheries Economics of the United States, 2012. NOAA 

Technical Memo NMFS-F/SPO-137. 175 pp.

4. Chesapeake Bay Program. “Agriculture.” <http://www.chesapeakebay.net/issues/issue/agriculture> 

Accessed 06/16/2015.

5. Murty, A.S. 1986. Toxicity of pesticides to fish. Volume 2. CRC Press. Boca Raton, Florida, USA. 

143 pp.

6. Chesapeake Bay Program. “Learn the Issues.” <http://www.chesapeakebay.net/issues> Accessed 

07/24/2015.

7. Leight, A., Jacobs, J., Gonsalves, L., Messick, G., McLaughlin, S., Lewis, J., Brush, J., Daniels, E., 

Rhodes, M., Collier, L. and Wood, B. 2014. Coastal Ecosystem Assessment of Chesapeake Bay 

Watersheds: A Story of Three Rivers - the Corsica, Magothy, and Rhode. NOAA National Ocean 

Service. Technical Memorandum NOS NCCOS 189. 96 pp.

8. Town of Centreville. “Centreville Maryland: Town History.” <http://www.townofcentreville.org/

government/history.asp> Accessed 09/01/2015.

9. Maryland Department of Planning. 2010. Maryland Population Density by Census Tract, 2010. 

Map.

10. Maryland Department of Natural Resources. 2003. Corsica River Watershed Characterization. 

Watershed Services Division. 80 pp.

11. Maryland Department of the Environment. “Maryland’s Searchable Integrated Report Database 

[Combined 303(d)/305(b) List].” <http://www.mde.state.md.us/programs/Water/TMDL/

Integrated303dReports/Pages/303d.aspx> Accessed 08/10/2015.

12. Maryland Department of Natural Resources. 2014. Corsica River 2014 Water Quality Report.

13. Multi-Resolution Land Characteristics Consortium. “National Land Cover Database.” <http://

www.mrlc.gov/index.php> Accessed 10/6/2015.

14. Thornton, P. 2007. “The Islands of the Magothy.” Maryland Life magazine. Great State Publishing 

September 5, 2007. 

15. The Nature Conservancy. 2013. Bathymetry of Chesapeake Bay. Bethesda, MD. Dataset.

16. Wheeler, T.B. 2005. “3 million gallons of sewage spill in river.” The Baltimore Sun. 

17. Maryland Department of Natural Resources. “Eyes on the Bay.” <http://mddnr.chesapeakebay.

net/> Accessed 10/6/2015.

18. Center for Watershed Protection. 2010. Summary of Findings from Rhode River Watershed Stream 

Corridor and Upland Assessments. 28 pp.

19. West-Rhode Riverkeeper. 2014. West & Rhode Rivers Report Card. 12 pp.
58

Chesapeake Bay Ecosystem Assessment References

20. Baltimore County Public Library. “The History of Essex & Middle River.” <http://www.bcpl.info/

community/history-essex> Accessed 07/24/2015.

21. Baltimore County Government. “Middle River Watershed.” <http://www.baltimorecountymd.gov/

Agencies/environment/watersheds/mrmain.html> Accessed 07/23/2015.

22. Versar Incorporated. “Water Quality Management Plan for Middle River Watershed.” 

<http://resources.baltimorecountymd.gov/Documents/Environment/Watersheds/

MiddleRiverExecSummary.pdf> Accessed 07/25/2015.

23. Hirsch, A. 2012. “Middle River conservation land targeted for housing growth.” The Baltimore Sun. 

24. Sassafras River Association. “Our Watershed.” <http://www.sassafrasriver.org/ourwatershed/> 

Accessed 08/06/2015.

25. Sassafras River Association and Center for Watershed Protection. 2009. Sassafras Watershed Action 

Plan. 255 pp.

26. The Nature Conservancy. “Nanjemoy Creek: An Emerald Green Oasis.” <http://www.nature.org/

ourinitiatives/regions/northamerica/unitedstates/maryland_dc/placesweprotect/nanjemoy-creek.

xml> Accessed 06/11/2015.

27. United States Geological Survey. “The National Map Viewer.” <http://viewer.nationalmap.gov/

viewer/> Accessed 07/24/2015.

28. Nanjemoy Creek Environmental Education Center. “Nanjemoy Creek Environmental Education 

Center.” <http://www.ccboe.com/schools/nanjemoycreek/> Accessed 08/10/2015.

29. Chesapeake Bay Foundation. 2013. Charles County Packet. 12 pp.

30. Murphy, R.R., Kemp, W.M. and Ball, W.P. 2011. Long-term trends in Chesapeake Bay seasonal 

hypoxia, stratification, and nutrient loading. Estuaries and Coasts 34: 1293-1309.

31. Hagy, J.D., Boynton, W.R., Keefe, C.W. and Wood, K.V. 2004. Hypoxia in Chesapeake Bay, 1950–

2001: Long-term change in relation to nutrient loading and river flow. Estuaries 27: 634-658.

32. Kimmel, D.G., Miller, W.D. and Roman, M.R. 2006. Regional scale climate forcing of 

mesozooplankton dynamics in Chesapeake Bay. Estuaries and Coasts 29: 375-387.

33. Wood, R. 2000. Synoptic scale climatic forcing of multispecies fish recruitment patterns in 

Chesapeake Bay. College of William and Mary. Virginia Institute of Marine Sciences. 163 pp.

34. Lipp, E.K., Schmidt, N., Luther, M.E. and Rose, J.B. 2001. Determining the effects of El NiñoSouthern Oscillation events on coastal water quality. Estuaries 24: 491-497.

35. National Climatic Data Center. “U.S. Climate Divisions.” National Oceanic and Atmospheric 

Administration. <http://www.ncdc.noaa.gov/monitoring-references/maps/us-climate-divisions.

php> Accessed 10/06/2015.

36. Florida Keys National Marine Sanctuary. “What is water quality?” <http://floridakeys.noaa.gov/

ocean/waterquality.html> Accessed 06/16/2015.
59

Chesapeake Bay Ecosystem Assessment References

37. Bricker, S., Longstaff, B., Dennison, W., Jones, A., Boicourt, K., Wicks, C. and Woerner, J. 2007. 

Effects of Nutrient Enrichment In the Nation’s Estuaries: A Decade of Change. National Centers 

for Coastal Ocean Science, Silver Spring, MD. NOAA Coastal Ocean Program Decision Analysis 

Series No. 26. 328 pp.

38. National Oceanic and Atmospheric Administration. “Natural Disturbances to Estuaries.” <http://

oceanservice.noaa.gov/education/tutorial_estuaries/est08_natdisturb.html> Accessed 06/16/2015.

39. National Oceanic and Atmospheric Administration. “Human Disturbances to Estuaries.” <http://

oceanservice.noaa.gov/education/tutorial_estuaries/est09_humandis.html> Accessed 06/16/2015.

40. National Oceanic and Atmospheric Administration. “Dissolved Oxygen.” <http://oceanservice.

noaa.gov/education/kits/estuaries/media/supp_estuar10d_disolvedox.html> Accessed 

06/16/2015.

41. United States Geological Survey. 2010. The National Water-Quality Assessment Program—Science 

to Policy and Management. 47 pp.

42. Integration and Application Network. “Chesapeake Bay Report Card.” <http://ian.umces.edu/

ecocheck/report-cards/chesapeake-bay/2013/> Accessed 10/06/2015.

43. Environmental Protection Agency. 2003. Ambient water quality criteria for dissolved oxygen, water 

quality and chlorophyll a for the Chesapeake Bay and its tributaries. Tech. Memo. 903-R-03-002. 343 

pp.

44. Chesapeake Bay Program. 2003. Technical Support Document for Identification of Chesapeake Bay 

Designated Uses and Attainability. EPA Report 903-R-03-004. 319 pp.

45. Anderson, D., Glibert, P. and Burkholder, J. 2002. Harmful algal blooms and eutrophication: 

nutrient sources, composition, and consequences. Estuaries 25: 704-726.

46. Chesapeake Bay Foundation. “Nitrogen & Phosphorus.” <http://www.cbf.org/how-we-save-thebay/issues/agriculture/nitrogen-phosphorus> Accessed 06/17/2015.

47. Wazniak, C.E., Hall, M.R., Carruthers, T.J.B., Sturgis, B., Dennison, W.C. and Orth, R.J. 2007. 

Linking water quality to living resources in a mid-Atlantic lagoon system, USA. Ecological 

Applications 17: S64-S78.

48. Messick, G., Jacobs, J., Brush, J., McLaughlin, S., Leight, A., Rhodes, M., Howard, D., Gonsalves, L. 

and Lewis, E. 2013. NCCOS coastal ecosystem assessment program: a manual of methods. National 

Oceanic and Atmospheric Administration. NOS NCCOS Technical Memorandum 169. 123 pp.

49. Ator, S.W., Brakebill, J.W. and Blomquist, J.D. 2011. Sources, fate, and transport of nitrogen and 

phosphorus in the Chesapeake Bay watershed: An Empirical model. US Department of the Interior, 

US Geological Survey. Scientific Investigations Report 2011–5167. 38 pp.

50. National Ocean Service. “Turbidity.” <http://oceanservice.noaa.gov/education/kits/estuaries/

media/supp_estuar10e_turbinity.html> Accessed 06/18/2015.

51. National Ocean Service. “What is a turbidity current?” <http://oceanservice.noaa.gov/facts/

turbidity.html> Accessed 06/18/2015.
60

Chesapeake Bay Ecosystem Assessment References

52. Lacouture, R.V., Johnson, J.M., Buchanan, C. and Marshall, H.G. 2006. Phytoplankton index of 

biotic integrity for Chesapeake Bay and its tidal tributaries. Estuaries and Coasts 29: 598-616.

53. National Ocean Service. “Chlorophyll.” <http://oceanservice.noaa.gov/education/kits/estuaries/

media/supp_estuar10h_clorophyll.html> Accessed 06/19/2015.

54. Wade, T.J., Pai, N., Eisenberg, J.N. and Colford, J.M., Jr. 2003. Do U.S. Environmental Protection 

Agency water quality guidelines for recreational waters prevent gastrointestinal illness? A systematic 

review and meta-analysis. Environ Health Perspect 111: 1102-1109.

55. American Public Health Association. 1998. Standard Methods for the Examination of Water and 

Wastewater, 20th Edition. American Public Health Association. 1325 pp.

56. Environmental Protection Agency. 2004. Water Quality Standards for Coastal and Great Lakes 

Recreation Waters; Final Rule. 40 CFR Part 131. 27 pp.

57. Baltimore County Department of Recreation and Parks. “Waterfront Parks.” <http://www.

baltimorecountymd.gov/Agencies/recreation/countyparks/waterfront/> Accessed 06/11/2015.

58. Zolper, T. “Forecast: clean, safe water for swimming, recreation through much of weekend.” 

<http://patch.com/maryland/annearundel/forecast-clean-safe-water-for-swimming-recreationthrough-much-of-weekend> Accessed 06/15/2015.

59. Magothy River Association. “Magothy River Association.” <http://www.magothyriver.org> 

Accessed 06/15/2015.

60. Kent County Office of Tourism Development. “Kent County Recreation: Paddling.” <http://www.

kentcounty.com/recreation/paddling/> Accessed 06/11/2015.

61. Kent County Office of Tourism Development. “Kent County Recreation: Paddling: Chester River 

South and Eastern Neck Island.” <http://www.kentcounty.com/recreation/paddling/chestersouth.

php> Accessed 06/15/2015.

62. Sindermann, C.J. 2005. Coastal pollution: effects on living resources and humans. CRC Press. 312 

pp.

63. Millikin, M.R. and Williams, A.B. 1984. Synopsis of Biological Data on the blue crab, Callinectes 

sapidus Rathbun. National Marine Fisheries Service. FAO Fisheries Synopsis No. 138. 43 pp.

64. Virnstein, R.W. 1977. The importance of predation by crabs and fishes on benthic infauna in 

Chesapeake Bay. Ecology 58: 1200-1217.

65. Howard, D.W., Lewis, E.J., Keller, B.J. and Smith, C.S. 2004. Histological techniques for marine 

bivalve molluscs and crustaceans. National Ocean Service. NOAA Technical Memorandum NOS 

NCCOS 5. 218 pp.

66. Lancia, R.A., Kendall, W.L., Pollock, K.H. and Nichols, J.D. 2005. Estimating the number of animals 

in wildlife populations. In: Techniques for Wildlife Investigations and Management. Braun, C.E. 

(ed), pp. 1-153. Wildlife Society. Bethesda, Maryland.

67. Chesapeake Bay Foundation. “Polluted Runoff.” <http://www.cbf.org/about-the-bay/issues/

polluted-runoff> Accessed 10/08/2015.
61

Chesapeake Bay Ecosystem Assessment References

68. Bohling, M. “Native fish spawning habitat: It’s more than just rocks in the river - Part 2.” Michigan 

State University Extension. <http://msue.anr.msu.edu/news/native_fish_spawning_habitat_

part_2_bohling15> Accessed 10/08/2015.

69. Montero, D., Izquierdo, M.S., Tort, L., Robaina, L. and Vergara, J.M. 1999. High stocking density 

produces crowding stress altering some physiological and biochemical parameters in gilthead 

seabream, Sparus aurata, juveniles. Fish Physiology and Biochemistry 20: 53-60.

70. Jacobs, J.M., Harrell, R., Uphoff, J., Townsend, H. and Hartman, K. 2013. Biological reference 

points for nutritional status of Chesapeake Bay striped bass (Morone saxatilis). North American 

Journal of Fisheries Management 33: 468-481.

71. Lafferty, K.D. and Kuris, A.M. 1999. How environmental stress affects the impacts of parasites. 

Limnology and Oceanography 44: 925-931.

72. McGrath, P. and Austin, H. 2009. Site fidelity, home range, and tidal movements of white perch 

during the summer in two small tributaries of the York River, Virginia. Transactions of the 

American Fisheries Society 138: 966-974.

73. Fournie, J.W., Summers, K.J., Courtney, L.A., Engle, V.D. and Blazer, V.S. 2001. Utility of splenic 

macrophage aggregates as an indicator of fish exposure to degraded environments. Journal of 

Aquatic Animal Health 13: 105-116.

74. Sindermann, C.J. 1979. Pollution-associated diseases and abnormalities of fish and shellfish: a 

review. Fish. Bull. 76: 717-749.

75. Austin, B. and Austin, D.A. 2007. Bacterial Fish Pathogens: Disease of Farmed and Wild Fish, 4th

Edition. Springer Science & Business Media. 552 pp.

76. Chesapeake Bay Program. “Bay Grasses.” <http://www.chesapeakebay.net/issues/issue/bay_

grasses#inline> Accessed 08/26/2015.

77. Virginia Institute of Marine Sciences. “SAV in Chesapeake Bay and Coastal Bays.” <http://web.

vims.edu/bio/sav/index.html> Accessed 08/26/2015.

78. Lippson, A.J. 1973. The Chesapeake Bay in Maryland: An Atlas of Natural Resources. Johns 

Hopkins University Press. Baltimore, MD. 55 pp.

79. Chesapeake Bay Program. “Underwater Bay Grass Abundance (Baywide).” <http://www.

chesapeakebay.net/indicators/indicator/bay_grass_abundance_baywide> Accessed 08/26/2015.

80. Chesapeake Bay Program. “Facts & Figures.” <http://www.chesapeakebay.net/discover/bay101/

facts> Accessed 06/16/2015.

81. Jordan, T., Pierce, J. and Correll, D. 1986. Flux of particulate matter in the tidal marshes and subtidal 

shallows of the Rhode River estuary. Estuaries 9: 310-319.