U.S. Department of the Interior

U.S. Geological Survey

Scientific Investigations Report 2005–5009

Effects of Best-Management Practices in Otter Creek 

in the Sheboygan River Priority Watershed, Wisconsin, 

1990−2002

In cooperation with the Wisconsin Department of Natural Resources
Effects of Best-Management Practices 

in Otter Creek in the Sheboygan 

River Priority Watershed, Wisconsin, 

1990−2002

By Steven R. Corsi, John F. Walker, Lizhu Wang, Judy A. Horwatich, and 

Roger T. Bannerman

In cooperation with the Wisconsin Department of Natural Resources

Scientific Investigations Report 2005–5009

U.S. Department of the Interior

U.S. Geological Survey
U.S. Department of the Interior

Gale A. Norton, Secretary

U.S. Geological Survey

Charles G. Groat, Director

U.S. Geological Survey, Reston, Virginia: 2005

For sale by U.S. Geological Survey, Information Services

Box 25286, Denver Federal Center

Denver, CO 80225

For more information about the USGS and its products:

Telephone: 1-888-ASK-USGS

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Any use of trade, product, or firm names in this publication is for descriptive purposes only and does not imply 

endorsement by the U.S. Government.

Cover photos (clockwise from top left):

Barnyard runoff control system with vegetation

Streambank fencing on Otter Creek

Barnyard runoff control system without vegetation

Contained walkway and stream crossing
iii

Contents

Abstract .................................................................................................................................................. 1

Introduction ........................................................................................................................................... 1

Purpose and Scope ..................................................................................................................... 2

Physical Setting and Land Use .................................................................................................. 2

Methods ................................................................................................................................................. 5

Hydrologic and Water Quality Data-Collection Network ...................................................... 5

Biological Data Collection .......................................................................................................... 5

Selection and Inventory of Watersheds .................................................................................. 8

Hydrologic Conditions During the Study Period .............................................................................. 8

Water Quality Before and After Implementation of Best-Management Practices ................. 15

Constituent Concentrations at Base Flow ............................................................................. 15

Storm Loads ................................................................................................................................ 17

Biological Data Before and After Installation of Best-Management Practices ...................... 20

Effects of Management Practices on Otter Creek ........................................................................ 21

Influence of BMPs on Water Quality ...................................................................................... 22

Influence of BMPs on Habitat and Fish ................................................................................. 23

Comparison of Results to Watershed Improvement Objectives ................................................. 23

Summary and Conclusions ................................................................................................................ 24

Acknowledgments .............................................................................................................................. 25

References Cited ................................................................................................................................ 25
iv

Figures

 1–4. Maps showing:

 1. Location of the Otter Creek, Meeme River, and Pigeon River Watersheds 

 and data-collection sites in Sheboygan and Manitowoc counties, Wis. ........... 3

 2. Land use and land cover in the Otter Creek Watershed, 

 Sheboygan County, Wis. .............................................................................................. 4

 3. Soil types in the Otter Creek Watershed, Sheboygan County, Wis. ..................... 6

 4. Best-management practices implemented during the study period in the 

 Otter Creek Watershed, Sheboygan County, Wis. .................................................. 9

 5–11. Graphs showing:

 5. Yearly precipitation throughout the study period and long-term average

 yearly precipitation at Plymouth and Sheboygan, Wis. ...................................... 10

 6. Cumulative rainfall distributions for the pre- and post-BMP (best-

 management practices) implementation period at Otter Creek, 

 Sheboygan County, Wis., for water years 1990–2002 ........................................... 10

 7. Annual streamflow, base flow, and stormflow at Otter Creek, 

 Sheboygan County, Wis., for water years 1990–2002 ........................................... 11

 8. Average monthly distribution of streamflow and total suspended solids, 

 total phosphorus, and dissolved ammonia nitrogen loads at Otter Creek, 

 Sheboygan County, Wis., for water years 1990–2002 ........................................... 12

 9. Average relative annual contributions of stormflow and base-flow 

 periods to streamflow, total suspended solids, total phosphorus, and 

 dissolved ammonia nitrogen loadings at Otter Creek, Sheboygan 

 County, Wis., for water years 1990–2002 ................................................................ 12

 10. Average monthly streamflow and loads of total suspended solids, total 

 phosphorus, and dissolved ammonia nitrogen during base flow and 

 stormflow periods, expressed as a percentage of the annual total water 

 volume and constituent loads at Otter Creek, Sheboygan County, Wis. ........... 14

 11. Concentrations and water-year medians of total suspended solids, total

 phosphorus, dissolved ammonia nitrogen, biochemical oxygen demand, 

 and fecal coliform in base-flow samples throughout the study period at 

 Otter Creek, Sheboygan County, Wis. ..................................................................... 16
v

Tables

 1. Summary of targeted and implemented rural best-management practices 

in the Otter Creek watershed, Sheboygan County, Wis. ............................................... 8

 2. Results of Wilcoxon rank-sum test for differences between constituent 

concentrations in base-flow samples from pre- and post-BMP implementation 

periods at Otter Creek, Sheboygan County, Wis. ........................................................ 17

 3. Regression results for storm loads from rainfall periods at Otter Creek, 

Wis., for combined and separate seasons .................................................................... 19

 4. Median rainfall-period storm loads and results of the Wilcoxon rank-sum 

test comparing storm-load residuals for pre- and post-BMP periods at Otter 

Creek, Wis. ......................................................................................................................... 19

 5. Average percent reductions predicted across all monitored storms by use 

of pre- and post-BMP regressions to estimate loads from rainfall periods 

at Otter Creek, Wis. ........................................................................................................... 20

 6. Results of trend analysis comparing habitat for pre- and post-BMP periods 

using analysis of covariance with the treatment station and reference 

stations, Otter Creek, Meeme River, and Pigeon River, Wis. ..................................... 21

 7. Results of trend analysis comparing fish community data for pre-and 

post-BMP periods using analysis of covariance with the treatment station 

and reference stations, Otter Creek, Meeme River, and Pigeon River, Wis. ........... 22
vi

Conversion Factors and Abbreviations

Multiply By To obtain

Length

inch (in.) 25.4 millimeter (mm)

foot (ft) 0.3048 meter (m)

mile (mi) 1.609 kilometer (km)

Area

acre 0.4047 square hectometer (hm2

)

square mile (mi2

) 2.590 square kilometer (km2)

Flow rate

cubic foot per second (ft3/s) 0.02832 cubic meter per second (m3/s)

Mass

pound, avoidupois (lb) 0.4536 kilogram (kg)

ton per day (ton/d) 0.9072 metric ton per day

Hydraulic gradient

foot per mile (ft/mi) 0.1894 meter per kilometer (m/km)

Temperature in degrees Celsius (°C) can be converted to degrees Fahrenheit (°F) as 

follows:

 °F = [1.8 x °C] + 32.

Concentrations of chemical constituents in water are given in milligrams per liter (mg/L).
Effects of Best-Management Practices in Otter Creek 

in the Sheboygan River Priority Watershed, Wisconsin, 

1990–2002

By Steven R. Corsi1, John F. Walker1, Lizhu Wang2, Judy A. Horwatich1, and Roger T. Bannerman2

Abstract

The U.S. Geological Survey and the Wisconsin 

Department of Natural Resources began a comprehensive, 

multidisciplinary evaluation-monitoring program in 1989 

to assess the effectiveness of the Wisconsin Nonpoint 

Source Program. Hydrologic, water-quality, habitat, and 

fish data were collected at Otter Creek from 1990 to 2002 

with the pre-BMP (best-management practice) period ending in September 1993 and the post-BMP period beginning 

in October 1999. BMPs installed in this basin included 

streambank protection and fencing, stream crossings, 

grade stabilization, buffer strips, various barnyard-runoff 

controls, nutrient management, and a low degree of upland 

BMPs. Reductions between pre- and post-BMP periods 

were detected in median concentrations of base-flow 

samples for total suspended solids and BOD5 but not for 

total phosphorus or dissolved ammonia nitrogen; fecal 

coliform concentrations in base-flow samples increased 

over the study period.

Reductions in rainfall storm loads between the preand post-BMP periods during the non-vegetative season 

(November through May) were detected for all three 

constituents monitored (total suspended solids, total phosphorus, and dissolved ammonia nitrogen). Differences in 

rainfall storm loads of these three constituents for the vegetative season (June through October) were not detected. 

When considering rainfall data from the entire year, reductions in storm loads were detected for total suspended 

solids and dissolved ammonia nitrogen (reductions were 

estimated at 58 percent for total suspended solids and 41 

percent for dissolved ammonia nitrogen). Annual reductions in rainfall storm loads for the non-vegetative season 

were estimated at 58 percent for total suspended solids, 

48 percent for total phosphorus, and 41 percent for 

dissolved ammonia nitrogen.

Habitat and fish data were collected each year of the 

study to track the effects of BMPs on stream habitat and 

fish communities. Final trend analysis was performed using 

habitat quality index scores, an index of biotic integrity, 

and some of the originally measured fish and habitat variables. Habitat was improved for stream segments that had 

either natural riparian buffer or where streambank fencing 

was installed, but not at the station where the riparian area 

was pasture and no streambank fencing was installed. The 

results also suggest that BMP implementation in Otter 

Creek substantially modified fish community structure, but 

the overall community quality was not improved. 

Introduction

Nonpoint-source contamination is a major contributor to water-resource-quality problems in Wisconsin. In 

recognition of the importance of nonpoint sources, the 

Wisconsin Nonpoint Source Water Pollution Abatement 

Program (Nonpoint Program) was enacted in 1978. When 

first introduced, the Nonpoint Program identified problems 

in 130 of the 330 watersheds in Wisconsin. For a given 

watershed, various management options—termed bestmanagement practices (BMPs)—are available for funding support through the Nonpoint Program. For example, 

practices in rural areas include conservation tillage, 

contour strip-cropping, streambank protection, and various 

barnyard-runoff controls. The Nonpoint Program provides 

matching funds to landowners for voluntary implementation of various BMPs using priority watersheds as a unit 

for consideration.

1 U.S. Geological Survey, Middleton, Wisconsin

2 Wisconsin Department of Natural Resources, Madison, Wisconsin
Until the late 1980s, very little data existed to demonstrate the effectiveness of BMPs for improving water 

quality in Wisconsin’s priority watersheds. The Wisconsin 

Department of Natural Resources (WDNR) and U.S. Geological Survey (USGS) developed and began a comprehensive, multidisciplinary evaluation-monitoring program in 

water year 1989 to assess the effectiveness of the Wisconsin Nonpoint Source Program (Wierl and others, 1996). 

This evaluation-monitoring program includes biological 

and stream-habitat monitoring by the WDNR and waterquality monitoring by the USGS. Eight watersheds were 

chosen for the evaluation-monitoring program. Results 

from two of these watersheds, Brewery and Garfoot Creeks 

in the Black Earth Creek Watershed, were published previously (Graczyk and others, 2003). This report presents 

results from Otter Creek, the third watershed where evaluation monitoring has been completed. These watersheds 

were chosen because WDNR and Land County Conservation District personnel felt that there existed a potential for 

significant improvement and because BMPs were scheduled to be installed within the project time frame. 

The USGS, in cooperation with the WDNR, studied 

the Otter Creek Watershed, a subbasin of the Sheboygan 

River, in eastern Wisconsin from September 1990 through 

September 2002 to assess the hydrology, biology, habitat, 

and water quality of Otter Creek and its tributaries. Streamflow and water-quality data were collected continuously at 

one station near the mouth of Otter Creek, while biology 

and habitat data were collected annually at four stations.

Purpose and Scope

This report summarizes the results of a study on 

effectiveness of watershed-management practices for controlling nonpoint-source contamination in the Otter Creek 

Watershed. Concentrations of total suspended solids, total 

phosphorus, dissolved ammonia nitrogen, 5-day biochemical oxygen demand (BOD5

), and fecal coliform in samples 

collected at base flow before BMP installation (pre-BMP) 

are compared and contrasted to those for the period after 

BMP installation (post-BMP). Pre-BMP storm loads of 

total suspended solids, total phosphorus, and dissolved 

ammonia nitrogen from sampled rainfall periods are 

compared and contrasted to the post-BMP storm loads. In 

addition, fish and habitat data are compared and contrasted 

between pre-BMP periods and post-BMP periods.

Data collection began in September 1990 and continued until September 2002. From September 1990 through 

September 30, 1993, BMPs were not installed in the Otter 

Creek watershed, and this time period is considered to be 

the pre-BMP period. Installation of BMPs began in 1993. 

In October 1999, BMP installation that was planned for this 

program was complete in the watershed. Monitoring after 

this time was considered to be the post-implementation 

period. For the purpose of this study, the post-BMP period 

is considered to be October 1999 through September 2002.

The overall objective of the WDNR and USGS evaluation-monitoring program was to evaluate BMP effectiveness in several small watersheds located in geographically 

and hydrologically diverse areas of Wisconsin. 

Physical Setting and Land Use

Otter Creek is a tributary to the Sheboygan River 

in Sheboygan County about 4 mi northeast of the city of 

Plymouth, Wis. (fig. 1). Otter Creek has been classified 

by the WDNR as a warm-water forage stream that has 

the potential to maintain a forage fish population and is 

suitable for partial body contact for recreational purposes 

(Wisconsin Department of Natural Resources, 1993). 

Otter Creek drains 9.5 mi2

 upstream from the streamgaging station near Plymouth, and the total stream length, 

including perennial and intermittent channels, is 13.0 mi 

from the station to the stream headwaters. The watershed 

contains several small lakes and ponds. The stream flows 

directly through two of the small lakes (first through Little 

Gerber Lake, then through Big Gerber Lake), which are 

connected by a short channel. These lakes are 7 acres and 

15 acres in surface area and have a maximum of 21 and 

37 ft in depth, respectively. The overall channel slope of 

Otter Creek is 25 ft/mi, and the channel slope between the 

10- and 85-percent points for the main channel is 23 ft/mi. 

The bed material consists mainly of sand, silt, and clay 

with gravel in riffle areas. The Otter Creek watershed has 

level to nearly level land slopes, a result of glacial scouring 

of the landscape. 

Total land use and land cover for Otter Creek is shown 

in figure 2. In the Otter Creek Watershed, cropland (62 percent) dominates the land use and land cover, with woodlots 

(14 percent) being the next greatest land use and land cover. 

Other substantial land use and land cover in Otter Creek 

includes grassland (10 percent) and wetlands (6 percent). 

In all, 64 farms are included in the Otter Creek Watershed. 

The average farm size is 140 acres, with an average of 129 

acres in crop production. There are eight barnyards in the 

watershed with an average herd size of 45 animals, all of 

which are dairy cows (Rappold and others, 1997). According to the Sheboygan County Land and Water Conservation Department, the number of livestock in the watershed 

and the cropland percentage has not changed substantially 

2 Effects of Best-Management Practices in Otter Creek in the Sheboygan River Priority Watershed, Wisconsin, 1990–2002
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Introduction 3
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Figure 2. Land use and land cover in the Otter Creek Watershed, Sheboygan County, Wis.

4 Effects of Best-Management Practices in Otter Creek in the Sheboygan River Priority Watershed, Wisconsin, 1990–2002
throughout the monitoring period, but exact numbers were 

not available. The soil types in the Otter Creek watershed 

vary spatially and consist mainly of silt loams to silty clay 

loams (fig. 3). These soils are well drained to somewhat 

poorly drained (Engel and others, 1978).

Methods

Watersheds can be affected in numerous ways by 

changes in land use and land management brought about 

by BMP installation. A suite of different variables were 

considered in an attempt to understand these effects. 

Hydrologic, water-quality, habitat, fish, and land-use data 

were the areas of study considered to be important for this 

evaluation. Not only are the areas of study important in 

this evaluation, but the exact methods of data collection 

and analysis are essential in detecting changes resulting 

from BMP installation. A description of data collection 

and analysis methods for each of these areas of study are 

included in this section.

Hydrologic and Water Quality DataCollection Network

A stream-gaging station equipped for continuous 

recording of data was installed in September 1990 at Otter 

Creek (fig. 1). Stage was measured with bubbler-type 

pressure transducers every 5 minutes during periods of 

increased runoff and every hour otherwise. Streamflow 

measurements were made according to standard USGS 

methods (Rantz and others, 1982) every 4 to 6 weeks, and 

more frequently during high flows, to define the stagestreamflow relation used to compute continuous streamflow record. 

The gaging station was equipped with a stage-activated refrigerated water sampler for automatic collection 

of water samples during periods of increased runoff from 

rainfall or snowmelt. The data logger was programmed 

to initiate sampling once the stream stage reached an 

initial sampling threshold. As stage increased, samples 

were collected with each 0.2-ft increase in stage; as 

stage decreased, samples were collected with each 0.3-ft 

decrease in stage. The sampling strategy was designed to 

collect more samples during increasing stage, when the 

concentration of the constituents of interest would likely 

be changing most rapidly. After a sampling event, the 

samples were collected from the gaging station, chilled on 

ice in coolers, processed at the USGS field office, and then 

transported to the Wisconsin State Laboratory of Hygiene 

to be analyzed for total suspended solids, total phosphorus, 

dissolved ammonia nitrogen, BOD5, and fecal coliform, 

using standard methods (Wisconsin State Laboratory of 

Hygiene, 1992, American Public Health Association, 

1989, 1992). Samples collected were selected for analysis to represent variation in water quality over a range of 

increasing and decreasing stages. 

In addition to the automated samples, manual samples 

were collected at a fixed interval. The fixed interval from 

the beginning of the study to August 1994 was approximately every 2 weeks in the spring, summer, and fall 

and once a month in the winter. After August 1994, the 

fixed interval was changed to weekly from April through 

October, twice per month in March and November, and 

monthly from December through February. Samples were 

integrated over the depth and width of the stream by use 

of a hand-held sampler (Edwards and Glysson, 1988). 

The fixed-interval samples also were analyzed for total 

suspended solids, total phosphorus, dissolved ammonia 

nitrogen, biochemical oxygen demand, and fecal coliform.

Precipitation was measured throughout the study 

period at three locations within the watershed (fig. 1). 

One rain gage was at the stream-gage location, and the 

other two rain gages were sited by trial and error to result 

in approximately equal Thiessen polygon areas. Thiessen 

polygons represent the areas in closest proximity to each 

rain gage; the average precipitation was computed as a 

weighted average using the Thiessen polygon areas as the 

weighting factor (Viessman and others, 1977). Precipitation was collected in an 8-in. collector that drained into a 

tipping bucket rain gage. Each tip represented 0.01 in. of 

rain; all rainfall data were recorded every 5 minutes. Rain 

gages were calibrated annually.

Biological Data Collection

Habitat and fish data were collected from Otter Creek 

and two reference streams. The reference watersheds 

were chosen to have similar characteristics in elevation, 

climate, surficial geology, soil, streamflow and temperature regimes, stream size, and stream segment gradient. 

Without human influence, Otter Creek and the reference 

streams would be expected to have similar water quality, 

physical habitat, and biological communities. 

Four sampling stations were established in the lower 

segment of the Otter Creek Watershed to monitor the 

effects of watershed BMP implementation on habitat and 

fish (fig. 1). Stations 1, 3, and 4 were located in heavily 

grazed pasture areas where the cattle had free access to 

the stream and the streambanks were severely trampled. 

Methods 5
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Figure 3. Soil types in the Otter Creek Watershed, Sheboygan County, Wis.

6 Effects of Best-Management Practices in Otter Creek in the Sheboygan River Priority Watershed, Wisconsin, 1990–2002
Station 3 was adjacent to a large barnyard that appeared to 

be a source of manure during runoff events. Station 2 was 

between stations 1 and 3 in a wooded riparian section of 

the stream. The streambanks along stations 1 and 3 were 

fenced in 1993 and 1996, respectively, to keep livestock 

off the streambanks and out of the stream. Station 4 was 

upstream from the other stations, and streambank fencing 

was not installed.

The reference streams, Meeme River and Pigeon 

River, drain 17.8 mi2

 and 14.7 mi2, respectively, at the 

furthest downstream sampling stations. Geographically, the 

reference watersheds are within 12 miles of Otter Creek. 

Meeme River is a tributary of the Pigeon River, which is 

tributary to Lake Michigan. Soil types in both reference 

watersheds are largely loams and silt loams as are soil 

types in the test stream. Both Meeme River and Pigeon 

River are third order, low gradient (5.8–14.8 ft/mi), warmwater streams. The Meeme and Pigeon Rivers have slightly 

higher proportions of agricultural land use (80 and 71 

percent) and lower percentages of vegetative land (12 and 

18 percent) in their watersheds compared with Otter Creek 

(the treatment stream). The riparian area for the Pigeon 

River was pasture for station 1 and narrow shrub buffer for 

station 2. The riparian area for the Meeme River was grass 

and shrub buffer. Both reference streams had barnyards in 

the upland of their watersheds. Two stations were sampled 

on each of the reference streams. There were no substantial 

land-use changes in the reference watersheds during the 

study years.

Sampling was done between July 30 and September 

11 each year when low streamflow facilitated sampling 

effectiveness and large-scale fish movement was unlikely 

(Lyons and Kanehl, 1993). Not all stations were sampled 

during each year, because a small number of stations were 

sampled in the initial years and more sampling stations 

were added as more resources became available in subsequent years. For Otter Creek, one station was sampled 

in 1990, two stations were sampled in 1991, and all four 

stations were sampled from 1992 to 2002. For the reference streams, one station was sampled between 1990 and 

1993, and two stations on each stream were sampled from 

1994 to 2002. 

Sampling station length was 35 times the mean 

stream width or a minimum of 328 ft, a distance sufficient 

to characterize the fish assemblage and to encompass 

about three meander sequences of the stream channel 

(Lyons, 1992; Simonson and others, 1994). Actual station 

lengths ranged from 344 to 768 ft. 

Various habitat variables were assessed at the sampling stations. Water turbidity, dissolved oxygen, specific 

conductance, and flow were measured at the downstream 

end of the station. Lengths of runs, riffles, and pools and 

the mean distances between bends and between riffles 

were determined for the entire station. Thirty habitat variables, encompassing channel morphology, bottom substrates, cover for fish, bank conditions, riparian vegetation, 

and land use were measured or visually estimated along 12 

evenly spaced transects by means of standardized procedures (Simonson and others, 1994). 

Fish sampling, consisting of a single upstream pass 

without block nets, was done within a day of habitat 

assessment. The entire length of each station was electrofished with a single tow-barge unit (Lyons and Kanehl, 

1993; Simonson and Lyons, 1995). During sampling, 

efforts were made to collect all fish greater than or equal to 

0.98 in. in total length observed, and all captured fish were 

identified to species, counted, weighted in species aggregates, and released back to the stream. 

Habitat data were summarized by calculating the 

mean and variance for each variable for each station in 

each year. From these variables, wetted-stream widthdepth ratio and habitat-quality index scores were computed 

by use of a system developed for Wisconsin stream fishes 

(Simonson and others, 1994). The overall habitat score 

was the sum of differentially weighted scores for the quality of riparian buffers, bank erosion, pool area, width-depth 

ratio, distance between riffles or bends, amount of fine 

sediment on the bottom, and cover for fish. 

 To summarize the fish data, computations were done 

for fish density (number per 328 ft of stream length) and 

percentages of individuals that were omnivores, insectivores, carnivores, simple lithophils, and tolerant and intolerant of environmental degradation (Lyons, 1996). Fish 

data were then used to compute an index of biotic integrity 

(IBI). The IBI applied here was specifically developed for 

Wisconsin warm-water streams and could range from 0 to 

100, with higher values indicating more environmentally 

sensitive fish communities (Lyons, 1996).

To evaluate how stream habitat and fish community 

changed through study years and how these variables 

responded to the implementation of BMPs, an analysis of 

covariance (ANCOVA) was done with reference data as 

covariance to isolate the effects of BMPs on habitat and 

fish from the effects of other factors, such as temporal 

climate changes that might have caused natural variation 

of stream habitat and fish communities. The ANCOVA, 

done by use of SAS (SAS institute Inc., 1990), is a type of 

multiple linear regression in which the relations of habitat 

and fish variables between reference and treatment streams 

were tested over time (Grabow and others, 1999). 

Methods 7
Selection and Inventory of Watersheds

Inventory of the rural watersheds began in 1992 

to provide information on land-use and land-treatment 

changes that may affect water quality. A geographic 

information system (GIS) database contained the land-use 

and BMP inventories. Watershed boundaries, hydrography, roads, streams, woodlots, rain gages, and BMPs were 

digitized from 1:24,000 topographic maps. Farm-field and 

parcel mapping was done by the USGS staff by digitizing 

orthophotos. Detailed descriptions of each watershed and 

the BMP program were reported in Rappold and others 

(1997), and Wierl and others (1996).

The Priority Watersheds Program selected, assessed, 

and approved the Sheboygan River project between 1985 

and 1991. Otter Creek is in the Sheboygan River Watershed and was administered under the Sheboygan River 

Priority Watershed project. Voluntary sign-up period 

for BMPs started in March 1989 and lasted until March 

1997. Monitoring of the post-BMP implementation began 

on October 1, 1999, after the majority of practices were 

installed and operational.

Targeted and implemented BMPs for the Otter Creek 

Watershed are summarized in table 1. Annual updates of 

practices—animal-waste management, streambank protection, and upland management—were obtained by contacting the Sheboygan County Land Conservation Department. 

Animal-waste management systems are installed to reduce 

the amount of organic matter reaching the stream by 

improving the cattle lots and adding filter strips. Streambank protection reduces the amount of sediment reaching 

the stream by limiting cattle access and stabilizing streambanks by various practices, including fencing and installation of watering areas in the stream. Upland-management 

practices reduce the amount of sediment and phosphorus 

by cropland and manure management on highly erodible 

lands. Upland-control practices include change in crop 

rotation, reduced tillage, critical area stabilization, grass 

waterways, and pasture management.

In 1999, a majority of the BMP installation goals set 

by the WDNR and local Land Conservation Department 

had been achieved in the Otter Creek Watershed. Additional practices could be implemented for several years, 

but it was felt that many sources of nonpoint pollution 

had been controlled by the practices that had been implemented and there were no immediate plans to implement 

more BMPs for sources that were not controlled. The 

land-use tracking was discontinued in 2002 when the postBMP monitoring phase ended. The status of barnyard and 

streambank-protection practices as of 2002 is shown in 

figure 4.

Wisconsin’s administrative rules to address the 

control of polluted runoff from rural areas are specified in 

NR120, “The Priority Watershed and Priority Lake Program”. The rules identify the most effective BMPs to control nonpoint pollutants. Those practices identified could 

be cost-shared up to 70 percent by the State of Wisconsin. 

The approximated cost for installation of BMPs in the 

Otter Creek Watershed was $675,000. About 60 percent of 

this funding was for animal-waste management practices, 

35 percent was for streambank practices and 5 percent for 

upland-management practices. It should be noted that most 

of the streambank buffering of Otter Creek was not funded 

by this program but rather by outside sources.

Hydrologic Conditions During the 

Study Period

Precipitation: The 30-year normal annual precipitation is 36.3 in. at the National Oceanic and Atmospheric 

Administration (NOAA) weather station in Plymouth, 

Wis., and 31.9 in. at the NOAA weather station in 

Sheboygan, Wis. (National Oceanic and Atmospheric 

Table 1. Summary of targeted and implemented rural bestmanagement practices in the Otter Creek watershed, 

Sheboygan County, Wis.

[BMP, best-management practice]

Management practice Targeted Implemented

Animal-waste management

Manure storage (facilities) 4 3

Barnyard-runoff control 

systems (facilities) 8 8

Milkhouse wastewater 

treatment (facilities) 0 2

Streambank protection

Streambank protection (feet) 6,600 6,220

Fencing (feet) 9,200 9,200

Stream crossings 

(number of crossings) 5 2

Grade stabilization 

(structures) 4 4

Buffer strips (acres) 0 19.76

Upland management

Targeted nutrient 

management (acres) 1,130 1,570

Targeted upland BMPs (tons 

of sediment)1 505 276

1 Upland BMPs include change in crop rotation, reduced tillage, critical 

area stabilization, grass waterways, and pasture management.

8 Effects of Best-Management Practices in Otter Creek in the Sheboygan River Priority Watershed, Wisconsin, 1990–2002
g

g

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g

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Figure 4. Best-management practices implemented during the study period in the Otter Creek Watershed, Sheboygan County, 

Wis.

Administration, 2000). Long term averages are 31.8 in. at 

Plymouth (1910 through 2002) and 30.8 in. at Sheboygan 

(1899 through 2002). Data collected at the NOAA gages 

indicate that precipitation during the study period was less 

than the long-term average for two of three years during 

the pre-BMP implementation phase and one of three years 

during the post-BMP implementation phase of the study 

(fig. 5). The largest deviation between annual precipitation 

and the long-term average was in calendar year 2000, 

when the precipitation was 42.6 in. at Sheboygan and 35.1 

in. at Plymouth. 

Monitored storms during the study period ranged in 

precipitation depth from 0.21 to 3.52 in. The median depth 

of precipitation from the monitored storms was greater 

during the pre-BMP implementation period (1.02 in.) than 

during the post-BMP implementation period (0.83 in.). 

The distribution of precipitation depth from monitored 

storms during the pre-BMP implementation period also 

indicates that the pre-BMP implementation-period storm 

depths were greater than those from the post-BMP implementation period (fig. 6). 

Streamflow: Streamflow data were collected continuously during the entire study period and published each 

Hydrologic Conditions During the Study Period 9
year in “Water Resources Data, Wisconsin” for water years 

1991 through 2002 (Holmstrom and others, 1992–2000, 

Garn and others, 2001, and Waschbusch and others, 2002–

2003). These data were used to determine streamflow 

characteristics and to compute nutrient and total suspended 

solids loads. In addition, daily mean base-flow contributions were separated from the daily mean streamflows 

(White and Sloto, 1990), and overland runoff (stormflow) 

was determined by computing the difference between daily 

mean streamflow and daily mean base flow. The mean 

annual streamflow at Otter Creek during the study period 

was 6.45 ft3/s, of which 75 percent was base flow (figs. 

7 and 9). The mean flow for the pre-BMP implementation period was 7.66 ft3

/s (76 percent base flow) and for 

the post-BMP implementation period was 6.69 ft3/s (75 

percent base flow). The greatest mean overall streamflow 

and base flow occurred in 1993.

Seasonal and Hydrologic Distribution of Loads:

Daily mass loads were computed for total suspended solids, total phosphorus, and dissolved ammonia nitrogen for 























02%#)0)4!4)/.).).#(%3

3HEBOYGAN

0LYMOUTH

0LYMOUTHLONG
TERMAVERAGEINCHES	

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TERMAVERAGEINCHES	

Figure 5. Yearly precipitation throughout the study period and long-term average yearly precipitation at Plymouth and 

Sheboygan, Wis.













    

0OST
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Figure 6. Cumulative rainfall distributions for the pre- and post-BMP (best-management practices) implementation period at 

Otter Creek, Sheboygan County, Wis.

10 Effects of Best-Management Practices in Otter Creek in the Sheboygan River Priority Watershed, Wisconsin, 1990–2002
















































































































!..5!,!6%2!'%$!),9-%!."!3%&,/7 "!3%&,/7!3!0%2#%.4!'%/&4/4!,!..5!,&,/7!..5!,!6%2!'%$!),9-%!.&,/7 !..5!,!6%2!'%$!),9-%!.25./&&4/4!,&,/7n"!3%&,/7	

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Figure 7. Annual streamflow, base flow, and stormflow at Otter Creek, Sheboygan County, Wis., for water years 1990–2002.

Hydrologic Conditions During the Study Period 11
the entire monitoring period. These values were used to 

compute mean monthly loads in order to understand how 

the loads were distributed throughout the year (fig. 8). The 

months during late winter and early spring contribute the 

greatest constituent loads at Otter Creek. The greatest total 

suspended solids loads were delivered in March and April 

with 41 percent of the mean annual load occurring in those 

2 months. An additional 29 percent of the mean annual 

total suspended solids load occurred during June and 

July, whereas the remaining eight months all contributed 

less than 8 percent per month. The three largest monthly 

contributions occurred during February, March, and April 

for both total phosphorus and dissolved ammonia (a total 

of 53 and 71 percent of the average annual load, respectively). 

3TREAMFLOW

4OTALSUSPENDEDSOLIDS

4OTALPHOSPHORUS

$ISSOLVEDAMMONIANITROGEN



















*!.5!29

&%"25!29

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$%#%-"%2

0%2#%.4!'%/&!..5!,4/4!,

Figure 8. Average monthly distribution of streamflow and total suspended solids, total phosphorus, and dissolved ammonia 

nitrogen loads at Otter Creek, Sheboygan County, Wis., for water years 1990–2002.



















3TREAMFLOW 4OTALSUSPENDED

SOLIDS

4OTAL

PHOSPHORUS

$ISSOLVED

AMMONIANITROGEN

#/.34)45%.4

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3TORMFLOW

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Figure 9. Average relative annual contributions of stormflow and base-flow periods to streamflow, total suspended solids, total 

phosphorus, and dissolved ammonia nitrogen loadings at Otter Creek, Sheboygan County, Wis., for water years 1990–2002.

12 Effects of Best-Management Practices in Otter Creek in the Sheboygan River Priority Watershed, Wisconsin, 1990–2002
Hydrologic Conditions During the Study Period 13

Additionally, streamflow and loads were separated 

into annual base-flow and stormflow contributions (fig. 9). 

Greater than 70 percent of streamflow contributions were 

during base-flow periods whereas the opposite was true 

for contributions of total suspended solids. Approximately 

59 percent of the mean annual total phosphorus load was 

contributed during stormflow periods. Dissolved ammonia 

load contributions were nearly equal during storm periods 

and base-flow periods.

Average monthly base-flow and stormflow contributions as a percentage of the annual total streamflow and 

constituent loads were computed to provide further insight 

into the mechanisms driving these parameters (fig. 10). 

• Streamflow. Average monthly base-flow contributions were greater than stormflow contributions for 

all months, with the peaks of both base-flow and 

stormflow volumes in March and April. 

• Total suspended solids. Average monthly contributions of total suspended solids loads were greater 

during storm periods than base-flow loads in all 

months except January, with the greatest contributions occurring during March, April, June, and July. 

• Total phosphorus. Average monthly loads were 

substantially greater in stormflow than in base flow 

for five months. Stormflow and base-flow loads 

were within 20 percent of each other during 6 

months, whereas January was the only month that 

average base-flow loads exceeded stormflow loads 

by more than 20 percent. 

• Dissolved ammonia nitrogen. Average monthly 

loads were dominated by the months of February 

and March, with base-flow contributions of 34 

percent and stormflow contributions of 29 percent 

of the mean annual load during those two months. 

Base-flow and stormflow contributions throughout 

the year were similar in magnitude on a month-bymonth basis.

The distribution of average monthly loads and 

average annual loads suggests that different constituents 

exhibit different behaviors depending on their particulate 

and dissolved fractions. Total suspended solids consists of 100 percent particulate matter, total phosphorus 

comprises both particulate and dissolved fractions, and 

dissolved ammonia nitrogen is completely in solution. 

Total suspended solids loads are dominated by stormflow; 

total phosphorus loads are greater in stormflow, but total 

phosphorus loads during base flow are more influential than those for total suspended solids; and dissolved 

ammonia nitrogen loads are equally influenced by stormflow and base flow. These data suggest that the constituents containing particulate fractions are most influential 

during stormflow and constituents containing dissolved 

fractions have increased influence during base flow. With 

this information and the monthly load data, it is apparent 

that the transport mechanisms and sources of these three 

constituents vary to some degree. Two primary pathways 

from sources to the stream are through surface runoff and 

ground-water discharge. The pathway of total suspended 

solids would be limited mainly to surface runoff, whereas 

the dissolved fractions of total phosphorus and ammonia nitrogen can also be transported through the shallow 

ground-water system and discharged to the stream in base 

flow. Solids will tend to settle out more during base-flow 

periods since stream velocities are lower during these 

periods than during storms. Also, the outlet to Big Gerber 

Lake will contain some phosphorus and dissolved ammonia nitrogen during base flow but most likely will have 

very little suspended solids. Average monthly concentrations of dissolved ammonia nitrogen in base flow and 

stormflow, as calculated by the monthly load divided by 

the monthly water volumes, are notably greater during 

January through March as compared to other months; in 

contrast, average monthly concentrations of phosphorus 

were similar throughout the year. Average monthly total 

suspended solids concentrations were lower during January and February than in other months and greatest during 

runoff periods in July. 

Higher concentrations and loads of dissolved 

ammonia nitrogen in winter could have several possible 

explanations, all based on the assumption that stream 

pH levels keep most dissolved ammonia nitrogen in the 

form of ammonium. First, winter spreading of manure on 

crop lands may result in greater concentrations and loads 

because infiltration would be reduced on frozen ground, 

microbial organisms needed for oxidation of ammonium would not be as active in cold winter temperatures, 

and contact with soils that have the potential to remove 

ammonium from the manure-influenced runoff would be 

reduced. Second, water from the outlet of Big Gerber Lake 

may have increased dissolved ammonia nitrogen if anoxic 

conditions exist in the lake during periods of ice cover. 

Data are not available to confirm this.

The implications of this information on identifying 

sources of individual constituents are as follows: Total 

suspended solids contributions would be greatest from 

areas of active surface runoff; land uses that promote 

infiltration would decrease total suspended solids loads. 

Total phosphorus and dissolved ammonia nitrogen would 
3TREAMFLOW

















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14 Effects of Best-Management Practices in Otter Creek in the Sheboygan River Priority Watershed, Wisconsin, 1990–2002

Figure 10. Average monthly streamflow and loads of total suspended solids, total phosphorus, and dissolved ammonia nitrogen 

during base flow and stormflow periods, expressed as a percentage of the annual total water volume and constituent loads at 

Otter Creek, Sheboygan County, Wis.
Water Quality Before and After Installation of Best-Management Practices 15

be greatest from areas of active surface runoff, but the 

dissolved fraction could also enter the stream through 

infiltration and subsequent ground-water transport to the 

stream; land uses that promote infiltration would reduce 

the phosphorus and dissolved ammonia nitrogen load 

during surface-runoff periods but may or may not change 

the total phosphorus and dissolved ammonia nitrogen load 

during base-flow periods. The Gerber lake system has 

potential to influence water quality, but more data would 

be necessary to quantify these influences. 

Water Quality Before and 

After Implementation of BestManagement Practices

The primary objective of this study was to evaluate 

overall BMP effectiveness at the watershed scale. BMPs 

implemented in the Otter Creek Watershed over the course 

of the study can potentially affect the stream in numerous 

different ways. Changes in water chemistry were evaluated 

using results from base-flow sampling and also by evaluating storm loads from rainfall periods. Numerous variables 

resulting from habitat and fish sampling were explored to 

evaluate changes in biology and factors directly affecting 

biology of the stream. Land-use data were used to interpret results from these analyses and to help understand the 

effects of individual BMP types. 

Constituent Concentrations at Base Flow

Base flow in Otter Creek consists of ground-water 

contributions and discharge from lake outlets in the watershed. Water-quality sample results from base-flow concentrations, therefore, will reflect a combination of lake and 

ground-water discharges and direct surface influence in 

the stream. Consequently, base-flow water quality may be 

affected by some land-use practices in the watershed that 

affect direct surface influences (such as streambank protection) and others that affect infiltration to ground water 

(such as filter strips). Big and Little Gerber Lakes will capture flows from upstream and slowly release those flows to 

Otter Creek at the outlet to the lakes. In this process, some 

particulate matter will settle out, reducing loads of total 

suspended solids and possibly nutrients at the outlet. For 

this reason, the watershed area upstream from the lakes 

will have less immediate effect on the stream conditions 

downstream from the lakes during periods of increased 

runoff, but the lakes would have a long-term effect during 

base flow.

Fixed-interval water-quality samples were collected 

throughout the pre- and post-BMP periods. Base-flow 

samples were separated from the fixed interval samples for 

use in subsequent data analysis. Base-flow samples were 

identified by use of a combination of techniques. First, 

daily mean streamflow was separated into base-flow and 

overland-runoff components. For any given fixed-interval 

sample, if the ratio of instantaneous discharge to daily 

mean base flow was less than or equal to 0.95, that sample 

was considered to be a potential base-flow sample. In addition, an estimation of the time lag for overland runoff in 

the watershed was computed as the drainage area in square 

miles raised to the exponent 0.2 (Viessman and others, 

1977). The overland-runoff time lag was determined to be 

2 days for Otter Creek, so potential base-flow samples that 

were collected within 2 days of the peak of a hydrograph 

were not considered to be base-flow samples.

A total of 184 samples were collected during base 

flow for total suspended solids, 184 for total phosphorus, 

183 for dissolved ammonia nitrogen, 175 for BOD5

, and 

151 for fecal coliform during the study (fig. 11). 

Statistical analyses (Wilcoxon rank-sum test) were 

used to test for significant differences between base-flow 

results from samples collected during the pre- and postBMP periods (Helsel and Hirsch, 1992). These analyses 

were done on three different temporal arrangements of 

the base-flow data: first with all pre- and post-BMP data, 

second with data from November through May (the nonvegetative season), and third with data from June through 

October (the vegetative season). Data from samples collected during the nonvegetative season were differentiated 

from data collected during the vegetative season to explore 

the possibility of seasonal differences in BMP effectiveness. 

Results of the Wilcoxon rank-sum nonparametric test 

indicate significant differences at the 95-percent confidence level between pre- and post-BMP base-flow 

concentrations for some constituents but not for others 

(table 2). Results from the data set with all base-flow 

samples included indicate a decrease in total suspended 

solids and BOD5

 concentrations, an increase in fecal 

coliform concentrations, and no detectable change in dissolved ammonia nitrogen and phosphorus concentrations. 

For samples collected during the nonvegetative season, 

results indicate a decrease in BOD5

 concentrations and 

no changes in the other four constituents. For samples 

collected during the vegetative season, a decrease is again 

noted in the BOD5

 concentrations, significant increases 

are shown for total phosphorus and fecal coliform, and no 

changes are detectable for dissolved ammonia nitrogen and 
Figure 11. Concentrations and water-year medians of total suspended solids, total phosphorus, dissolved ammonia nitrogen, 

biochemical oxygen demand, and fecal coliform in base-flow samples throughout the study period at Otter Creek, Sheboygan 

County, Wis.

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16 Effects of Best-Management Practices in Otter Creek in the Sheboygan River Priority Watershed, Wisconsin, 1990–2002
Table 2. Results of Wilcoxon rank-sum test for differences between constituent concentrations in base-flow samples from preand post-BMP implementation periods at Otter Creek, Sheboygan County, Wis. 

[mg/L, milligrams per liter; BMP, best-management practice; bold text indicates a statistically significant change in concentration between pre- and postBMP implementation periods]

Response variable

Number of 

samples for 

pre-/postBMP periods

Median concentration

(mg/L)

Pre-BMP Post-BMP Significance level

Combined seasons

Total suspended solids 40/40 9.0 5.2 0.02/decrease

Total phosphorus 40/41 0.07 0.074 0.052

Dissolved ammonia nitrogen 40/41 0.0325 0.022 0.06

Biochemical oxygen demand 39/37 2.0 1.1 0.0001/decrease

Fecal coliform 34/37 550 2,000 0.0002/increase

Nonvegetative season

Total suspended solids 21/11 9.0 7.0 0.11

Total phosphorus 21/11 0.07 0.061 0.088

Dissolved ammonia nitrogen 21/11 0.053 0.03 0.066

Biochemical oxygen demand 20/11 2.2 1.3 0.001/decrease

Fecal coliform 18/11 490 810 0.13

Vegetative season

Total suspended solids 19/29 9.0 5.0 0.29

Total phosphorus 19/30 0.06 0.082 0.004/increase

Dissolved ammonia nitrogen 19/30 0.018 0.021 0.36

Biochemical oxygen demand 19/26 1.8 1.1 0.029/decrease

Fecal coliform 16/26 675 2,250 0.0013/increase

Water Quality Before and After Installation of Best-Management Practices 17

total suspended solids. There is agreement from analysis 

of all three data sets that the concentration of BOD5 has 

decreased in base flow from the pre- to post-BMP periods 

with a reduction in median concentrations of 45 percent. 

The medians of total suspended solids concentrations are 

also reduced from the pre- to post-BMP periods, but this 

difference is statistically significant only in the overall 

data set and not in the vegetative or the nonvegetative 

seasonal data sets. This result could be due to the reduced 

sample size and the large variability of total suspended 

solids data in the seasonal data sets, as compared to only 

22- and 34-percent reductions in median concentrations. 

The medians of base-flow concentrations for dissolved 

ammonia nitrogen are reduced from the pre- to the postBMP periods in the overall data set and the data collected 

during the nonvegetative season, but they remain nearly the 

same for samples collected during the vegetative season. 

None of these results prove to be statistically significant 

at the 95-percent confidence level even though the overall 

median dissolved ammonia nitrogen concentration shows 

a 32-percent reduction from the pre- to the post-BMP periods. The increase in median fecal coliform concentrations 

is significant for the overall data set and for samples collected during the vegetative season. This result is notable, 

with an increase of 260 percent from the pre- to the 

post-BMP periods. The cause of this sharp increase has not 

been determined. Overall total phosphorus concentrations 

in base flow do not seem to change significantly except for 

a 37-percent increase during the vegetative season. 

Storm Loads

Because much of the annual total suspended-solids 

and nutrient transport occurs during storms, fixed-interval 

sampling—particularly at a monthly frequency—may 

not show changes resulting from BMP implementation 

(Walker, 1993). Consequently, mass transport resulting 

from individual rainfall storms was analyzed. Stream water 

was sampled numerous times per storm for each storm 

used in the analysis (average of 8 samples per storm, minimum of 2 samples per storm, and maximum of 29 samples 

per storm). Instantaneous mass transport of a particular 

constituent was determined by multiplying streamflow by 

the concentration of the constituent and a conversion factor 
18 Effects of Best-Management Practices in Otter Creek in the Sheboygan River Priority Watershed, Wisconsin, 1990–2002

(Porterfield, 1972). The integration method was then used 

to determine the mass transport of each constituent for 

each storm (Porterfield, 1972), expressed as a storm load. 

Concentration at the beginning of a storm was estimated 

from samples collected during previous base-flow periods 

between storms. Concentration at the end of the storm was 

estimated from samples collected immediately after the 

end of the storm. Some concentration data for individual 

storms were estimated by the relation between concentration and streamflow. These estimates were kept to a 

minimum. 

In many cases, the variability in the storm loads is 

large enough to mask potential differences in the pre- and 

post-BMP periods. In addition, because the pre- and postBMP periods arise from different hydrologic conditions, 

differences in the hydrologic conditions could result in differences that are not a result of the management practices. 

For these reasons, one solution is to perform regressions 

relating the storm loads to variables representing climatic 

and seasonal conditions. If the explanatory variables 

remove variability representing the natural climatologic 

and seasonal conditions, then the variability remaining 

in the regression residuals represents the combination of 

changes induced by the BMPs and model error. Because 

the regression, by design, reduces the variability in the 

data, it should theoretically be possible to detect smaller 

differences between the pre- and post-BMP periods than to 

detect differences in the storm loads.

Several explanatory variables were selected for use 

in the regressions, most of which were based on various 

measures of precipitation for each distinct rainfall storm. 

These included total rainfall (P), the 15- and 30-minute 

maximum intensities (I15 and I30), and the Universal Soil 

Loss Equation (USLE) erosivity index (EI) (Wischmeier 

and Smith, 1978). Additional precipitation-based measures 

included the 1-, 3-, and 5-day antecedent precipitation 

(API1

, API3, and API5), which is computed as the total 

rainfall for the 1, 3, and 5 days prior to the beginning of 

each storm, respectively. Terms combining total rainfall 

and the antecedent precipitation also were considered 

(for example, P+API1). Finally, two seasonal terms were 

included to allow for variations arising solely on the basis 

of the time of year. The seasonal terms were based on the 

serial date of the storm (T), using a period of 1 year and 

both sine and cosine terms to allow for amplitude and 

phase-shift estimation.

Because hydrologic conditions and, hence, constituent loads can be quite different because of crop cover, a 

further seasonal distinction was used. The period from 

June 1–October 31 represents the time when more vegetation is present than the remainder of the year. Separate 

analyses were done for these two seasons.

Preliminary regression results indicated that, for many 

of the constituents and storms, simple linear regressions 

resulted in the prediction of negative storm loads. Because 

this would result in erroneous conclusions when comparing pre- and post-BMP periods, the final regressions were 

based on a logarithmic transformation of the storm loads, 

thus assuring that negative loads cannot be predicted. 

For each constituent, stepwise regressions were done 

on the explanatory variables described above (table 3). For 

each regression, additional variables were considered if the 

improvement in the resulting regression was considered 

large enough to warrant their use (a coefficient significantly different from zero at the 95-percent confidence 

level). In addition, various regression plots were examined 

to verify that the underlying assumptions of regression 

analysis were not violated. 

The regression residuals also were tested for differences between the pre- and post-BMP periods (table 4). 

The median storm loads from rainfall periods for all three 

constituents for the pre-BMP and post-BMP periods are 

also listed in table 4. Regression residuals for the two periods were compared statistically by means of the Wilcoxon 

rank-sum test, as described previously. If the regressions 

represent variability due to natural factors, a difference in 

the regression residuals could be attributed directly to a 

difference due to the BMPs.

For combined seasons, all median storm loads from 

rainfall periods decreased. Testing the storm-load residuals 

demonstrates that this decrease is statistically significant 

for both total suspended solids and dissolved ammonia 

nitrogen at the 95-percent confidence level (table 4), but 

not for total phosphorus. Therefore, for total suspended 

solids and dissolved ammonia nitrogen, the difference in 

pre- and post- BMP conditions is likely due to the BMPs 

installed.

For the nonvegetative season, again all median storm 

loads from rainfall periods decreased. The storm-load 

residuals demonstrate that this difference is statistically 

significant for all three constituents (table 4). For the vegetative season, all median storm loads from rainfall periods 

decreased, but none of these differences were statistically 

significant at the 95-percent confidence level based on 

storm-load residuals. Differences in median storm loads 

from rainfall periods for the pre- and post-BMP conditions 

in the nonvegetative season are likely due to installation 

of BMPs; however, in the case of the vegetative season, 

the decrease in median storm loads from rainfall periods 

was not verified with these statistical tests, so it may have 
Table 4. Median rainfall-period storm loads and results of the Wilcoxon rank-sum test comparing storm-load residuals for preand post-BMP periods at Otter Creek, Wis.

[Total suspended-solids loads are in tons; BMP, best-management practice; bold text indicates a statistically significant change in concentration between 

pre- and post-BMP implementation periods; lbs, pounds]

Median storm loads Storm-load residuals

Variable Pre-BMP Post-BMP Significance level

Combined seasons

Total suspended solids (tons) 8.3 3.0 0.031

Total phosphorus (lbs) 69.4 30.3 0.186

Dissolved ammonia nitrogen (lbs) 32.6 13.4 0.037

Nonvegetative season

Total suspended solids (tons) 11.9 4.1 0.0047

Total phosphorus (lbs) 75.7 54.4 0.038

Dissolved ammonia nitrogen (lbs) 34.8 20.1 0.028

Vegetative season

Total suspended solids (tons) 8.3 2.2 0.802

Total phosphorus (lbs) 57.0 25.4 0.770

Dissolved ammonia nitrogen (lbs) 18.5 8.5 0.319

Table 3. Regression results for storm loads from rainfall periods at Otter Creek, Wis., for combined and separate seasons.

[In, n-minute maximum precipitation intensity; P, total precipitation; APIn, n-day antecedent precipitation; T, serial date of storm; R2, fraction of the 

variance of response variables explained by the explanatory variables for the model]

Response variable Explanatory variables Sample size Adjusted R2 Standard

error

Standard error 

(percent)

Combined seasons

Total suspended solids I30, P+API1

, P+API5, cos(T) 61 0.573 1.19 149

Total phosphorus I15, P+API1

, P+API5, sin(T) 61 .536 .832 93.1

Dissolved ammonia nitrogen P+API1

, P+API5, sin(T), cos(T) 60 .546 .691 74.7

Nonvegetative season

Total suspended solids P+API1

, cos(T) 31 0.436 1.32 174

Total phosphorus P+API5

, sin(T), cos(T) 31 .520 .705 76.5

Dissolved ammonia nitrogen P+API5

, sin(T), cos(T) 31 .514 .680 73.4

Vegetative season

Total suspended solids P+API5

, sin(T) 30 0.652 1.12 137

Total phosphorus P+API5

, sin(T) 30 .529 .973 113

Dissolved ammonia nitrogen P+API5

, sin(T) 29 .423 .732 79.9

Water Quality Before and After Installation of Best-Management Practices 19
Table 5. Average percent reductions predicted across all monitored storms by use of pre- and post-BMP regressions to 

estimate loads from rainfall periods at Otter Creek, Wis.

[BMP, best-management practice]

Season

Variable Nonvegetative

(percent)

Vegetative

(percent)

Combined

(percent)

Total suspended solids 73 41 58

Total phosphorus 61 34 48

Dissolved ammonia nitrogen 42 40 41

20 Effects of Best-Management Practices in Otter Creek in the Sheboygan River Priority Watershed, Wisconsin, 1990–2002

been due to something other than BMP implementation. 

One possibility is that hydrologic conditions were different 

between rainfall storms monitored during the vegetative 

seasons of the pre- and post-BMP periods.

The difference between pre- and post-BMP median 

storm loads from rainfall periods does not really reflect the 

percentage reduction in the individual rainfall storm loads 

largely because the pre- and post-BMP periods monitored 

different hydrologic conditions. Use of separate pre- and 

post-BMP regressions allows prediction of the theoretical pre- and post-BMP storm loads from rainfall periods 

for different values of the explanatory variables. For these 

conditions, the difference in the loads predicted by the preand post-BMP regressions represents the theoretical reduction in load. All explanatory variables with a coefficient 

significantly different from zero at the 95-percent confidence level were included in the regressions; all regressions were significant at the 95-percent confidence level. 

The regressions computed for the pre-BMP conditions 

were then used to predict what the theoretical pre-BMP 

load would have been for the explanatory variables for 

all of the monitored rainfall storms. Likewise, the regressions computed for the post-BMP conditions were used 

to predict the theoretical post-BMP storm loads for all the 

monitored rainfall storms. The percentage reduction was 

then computed based on the theoretical pre- and post-BMP 

loads, and averaged across all of the monitored rainfall 

storms. In a few cases, the theoretical post-BMP load 

exceeded the theoretical pre-BMP load. This is not surprising, as separate regressions were computed for the pre- and 

post-BMP conditions, and for most of the regressions the 

explanatory variables differed slightly. This occurred for 

less than 10 percent of the storms, and the resulting negative percent reductions were included in the calculation 

of the average percent reduction for each constituent. The 

resulting average percent reductions of monitored rainfall 

storms for the entire study period for separate and combined seasons are given in table 5.

Biological Data Before and After 

Installation of Best-Management 

Practices

Variations in stream channel morphology, substrate 

composition, and overall fish-habitat condition for Otter 

Creek and the reference streams were considerable. During the early sampling years (1990–93), the variation was 

greater than during the rest of the study years. For example, embeddedness varied 76 percent in the first three years 

as compared to 25 percent in the remaining years for station 1 at Otter Creek, 78 percent as compared to 21 percent 

for station 1 at Pigeon River, and 32 percent as compared 

to 26 percent for station 1 at Meeme River. Cobble and 

gravel substrates varied 34 percent in the first three years 

and 26 percent during the remaining years for Otter Creek, 

51 percent as compared to 29 percent for Pigeon River, and 

29 percent as compared to 21 percent for Meeme River. 

Pigeon River stations and Otter Creek station 4 varied 

more than the other stations. These stations had narrower 

and deeper channels than other sampled stations.

ANCOVA indicated that the overall stream-habitat 

quality in Otter Creek was improved by BMP implementation for stream segments that had either natural riparian 

buffer or stream segments where streambank fencing was 

installed (table 6). For stations 1, 2, and 3, eight of the ten 

monitored habitat variables were significantly improved 

(at the 95-percent confidence level) by BMP implementation. Substrate embeddedness, bank erosion, sediment 

depth, silt and sand substrates, and width-depth ratio were 

negatively correlated with BMP implementation. Conductivity, gravel and rubble substrates, and overall habitat 
Table 6. Results of trend analysis comparing habitat for pre- and post-BMP periods using analysis of covariance1

 with the treatment station and reference stations, Otter Creek, Meeme River, and Pigeon River, Wis.

[BMP, best-management practice; P, significance level; R2, fraction of the variance of response variables explained by the explanatory variables for the 

model; μs/cm, microsiemens per centimeter; %, percent; m, meters; e, error; Y, variable value of treatment site; X1, variable value of paired reference 

sites; X2, years since BMP implementation; βo, constant; β1; change in Y per unit change in X1 when holding X2 constant; β2, change in Y per unit change 

in X2 when holding X1 constant; bold values indicate a significant change in habitat variables (p < 0.05)]

Habitat variables βo β1 β2 Pβ1 Pβ2 R2

model Pmodel

Test sites 1 to 3

Specific conductance 

(μs/cm) 561 -0.03 17.8 0.871 0.008 0.90 0.009

Embeddedness (%) 6.33 1.01 -2.86 0.332 0.017 0.89 0.012

Bank erosion (%) 16.98 -0.03 -1.51 0.968 0.049 0.48 0.074

Rubble and gravel (%) 31.66 0.26 6.05 0.554 0.017 0.85 0.019

Riffle (%) -0.97 0.76 1.32 0.224 0.103 0.67 0.114

Cover for fish (%) -1.72 0.25 0.07 0.015 0.831 0.84 0.026

Sediment depth (m) 0.02 0.04 -0.01 0.803 0.044 0.73 0.069

Silt and sand (%) 45.5 0.20 -3.12 0.657 0.015 0.85 0.023

Width to depth ratio 14.4 0.38 -0.32 0.362 0.019 0.83 0.380

Habitat score 6.80 0.65 1.11 0.035 0.028 0.85 0.022

Test site 4 

None of the above variable changes were significantly correlated to BMP implementation for site 4

1 (Y = βo

 + β1 * X1 + β2 * X2 + e)

Effects of Management Practices on Otter Creek 21

scores were positively correlated with BMP installation. 

The changes in percentages of riffle and cover for fish 

were not correlated with BMP implementation. In contrast, 

none of the habitat variable changes were correlated with 

BMP implementation at station 4 where riparian area was 

pasture and no streambank fencing was installed.

Fish abundance decreased in treatment- and reference-stream assessment sites during the 13 sampling 

years. Comparison of data from the first 3 years and the 

last 3 years showed that total fish abundance decreased 

79 percent in Otter Creek and 65 percent in the reference 

streams. When all sampling years were considered, the 

percentages of tolerant fishes and omnivores increased 

in Otter Creek, whereas tolerant fishes decreased and 

insectivores increased in reference streams. Percentage of 

intolerant fishes and IBI score showed no obvious trend in 

Otter Creek or in reference streams.

When data from paired reference streams were 

incorporated as covariance to detect BMP influence on the 

treatment stream, ANCOVA indicated that fish abundance 

significantly decreased and percentage omnivore individuals increased in Otter Creek stations with natural or 

fenced riparian areas (table 7). Number of fish species and 

percentage of darter individuals significantly decreased in 

station 4 where the riparian area was pasture. None of the 

changes for the other evaluated variables was attributed to 

BMP implementation.

Effects of Management Practices on 

Otter Creek

Concentrations of nutrients and total solids observed 

during base flow and storms can be reduced by BMPs. For 

the purpose of discussion, BMPs can be divided into five 

main categories: animal-waste systems, fencing, streambank protection, nutrient-management, and upland-management practices. The Otter Creek Watershed is affected 

by a mixture of BMPs, and each BMP has varying success 

in controlling different aspects of the water quality, habitat, 

and biology of the stream. A description of individual 

BMPs and their potential effects on water quality has been 

previously published (Graczyk and others, 2003). Changes 

in fish communities would depend on a combination of 

changes in water quality and habitat.
Table 7. Results of trend analysis comparing fish community data for pre-and post-BMP periods using analysis of covariance1

with the treatment station and reference stations, Otter Creek, Meeme River, and Pigeon River, Wis.

[BMP, best-management practice; P, significance level; R2, fraction of the variance of response variables explained by the explanatory variables for the 

model; %, percent; ft, feet; e, error; No., number; Y, variable value of treatment site; X1, variable value of paired reference sites; X2, years since BMP 

implementation; βo, constant; β1; change in Y per unit change in X1 when holding X2 constant; β2, change in Y per unit change in X2 when holding X1

constant; bold values indicate a significant change in habitat variables (p < 0.05)]

Fish variables βo β1 β2 Pβ1 Pβ2 R2

model Pmodel

Test sites 1 to 3

Number of species 7.08 0.61 -0.71 0.157 0.098 0.49 0.192

Abundance (No./328 ft) 964 0.07 -68.5 0.684 0.017 0.73 0.019

Index of biotic integrity 29.2 0.62 -2.23 0.252 0.181 0.44 0.178

Darter individuals (%) 10.9 0.24 -0.65 0.528 0.133 0.40 0.214

Intolerant individuals (%) 1.80 -0.38 -0.11 0.715 0.353 0.26 0.385

Omnivore individuals (%) 3.08 0.07 2.24 0.729 0.002 0.87 0.002

Insectivore individuals (%) 29.8 0.20 -1.19 0.385 0.341 0.15 0.611

Lithophil individuals (%) 49.8 0.19 -1.29 0.556 0.193 0.44 0.172

Tolerant individuals (%) 40.9 0.30 1.47 0.193 0.154 0.31 0.317

Test site 4

Number of species 13.2 0.42 -0.72 0.461 0.045 0.60 0.064

Darter individuals (%) 22.5 -0.31 -1.39 0.562 0.033 0.56 0.086

None of the other variable changes were significantly correlated to BMP implementation 

1 (Y = βo

 + β1 * X1 + β2 * X2 + e)

22 Effects of Best-Management Practices in Otter Creek in the Sheboygan River Priority Watershed, Wisconsin, 1990–2002

Influence of BMPs on Water Quality

Sampling results indicate an overall improvement 

in water quality as a result of BMP implementation in 

the Otter Creek Watershed. Base-flow concentrations 

were significantly reduced for total suspended solids and 

BOD5. These reductions were most likely caused by the 

installation of streambank fencing reducing the number of 

livestock in the stream, barnyard-runoff control systems, 

manure storage facilities, and milk house wastewater 

treatment systems. There was also a septic system connection to a drain tile that was disconnected in the summer of 

1999. Median concentrations of dissolved ammonia nitrogen decreased, but neither total phosphorus nor dissolved 

ammonia nitrogen concentrations of samples collected 

during base-flow periods resulted in statistically significant 

differences from pre- to post-BMP periods. The reason 

for this result is uncertain considering the high level of 

nutrient management in the watershed, but this absence of 

change could be due to the already low concentrations of 

total phosphorus and dissolved ammonia nitrogen during 

base flow (table 2, fig. 11). Base-flow concentrations of 

total phosphorus and dissolved ammonia nitrogen during 

the pre-BMP period were below 0.2 mg/L except in one 

sample for dissolved ammonia nitrogen. Fecal coliform 

concentrations increased from the pre- to the post-BMP 

period. The cause of this result is uncertain.

 Storm loads from rainfall periods in Otter Creek 

were significantly reduced for all three monitored waterquality constituents, as indicated by differences in stormload residuals (table 4). There are clear differences in 

the results between the nonvegetative and the vegetative 

seasons. Results from rainfall storms monitored during the 

nonvegetative season show significant reductions from the 

pre-BMP to the post-BMP period in storm loads of total 

suspended solids, total phosphorus, and dissolved 

ammonia nitrogen. Although median storm loads from 

rainfall periods are smaller in data from the vegetative 

season, none of these differences prove to be statistically 

significant. 

Comparison of a combined data set from both the 

vegetative and the nonvegetative season shows significant 

reductions in total suspended solids and dissolved ammonia nitrogen storm loads from rainfall periods, as indicated 

by differences in storm-load residuals. The median total 

phosphorus storm load is reduced by 56 percent, yet this 
Comparison of Results to Watershed Improvement Objectives 23

reduction is not statistically significant. This is most likely 

caused by a large scatter around the regression line, a lack 

of representative explanatory variables that adequately 

describe conditions needed to generate total phosphorus 

contributions to the stream, or a combination of these two 

factors.

Reductions in monitored constituents could have been 

due to a combination of factors. There were numerous 

BMPs installed during the study period, including animalwaste management systems, streambank protection, and 

upland-management practices. Since individual monitoring 

was not done for each BMP, it is not possible to quantitatively determine the effect of each type of BMP, but Sheboygan County Land and Water Conservation Department 

personnel assessed each of these BMPs and felt that the 

most effective BMPs for total suspended solids reduction 

were the buffer strips which provide an area for solids to 

settle before reaching the stream, and streambank fencing 

that allows for growth of vegetation on the streambank, 

reducing streambank erosion. For reductions in nutrients, 

it was felt that the most effective BMPs were streambank 

fencing which reduced the number of livestock in the 

stream, barnyard-runoff control systems, manure-storage 

facilities, and milk house wastewater treatment systems. 

Influence of BMPs on Habitat and Fish

Habitat- and fish-sampling results imply that implementation of BMPs in Otter Creek improved overall 

stream physical-habitat conditions as represented by 

habitat score. However, only stream segments where there 

was natural riparian vegetative buffer or where stream buffers had been installed as a riparian BMP showed obvious 

improvement. Results also suggest that BMP implementation in Otter Creek substantially modified fish-community 

structure, but the overall community quality represented 

by IBI and percentage of intolerant individuals was not 

improved. The actual changes in the stream that are 

responsible for these changes in fish-community structure 

could be due to the observed habitat change, but available 

data do not allow for a cause-effect determination.

It is not fully understood why BMPs have improved 

habitat but have not improved fish communities in Otter 

Creek after more than five years of BMP implementation. 

One possible explanation is that streambank fencing and 

the regrowth of vegetation in the riparian areas at Otter 

Creek stations 1 and 3 have reduced bank erosion and narrowed and deepened the stream channel. This is evidenced 

by a decrease in the width to depth ratio and bank erosion 

(The coefficient β2 is significant and β2 < 0 for width 

to depth ratio and bank erosion in table 6). This channel 

morphological change further increases current velocity and, therefore, results in an increase in substrate size 

and a decrease in embeddedness. However, such habitat 

improvements have not been seen at the other stream sections that have no natural vegetative buffer or streambank 

fencing (for example, station 4). Even if sediment input 

from the watershed is reduced, the sediment accumulated 

inside the stream in the segment without riparian BMPs 

will continue to influence the habitat use by fishes in the 

improved stream sections; therefore, the overall process 

of improving fish community may take much longer 

than initially expected. It is apparent that more years and 

detailed environmental data would be necessary for causal 

inference of factors determining fish population levels 

and variability and for understanding the organizational 

mechanism of the stream system. 

Comparison of Results to Watershed 

Improvement Objectives

In the Nonpoint Source Control Plan for the Sheboygan River Priority Watershed Project (Wisconsin Department of Natural Resources, 1993), the specific objectives 

for the Otter Creek subwatershed are the following:

1. Maintain the current forage fishery classification. 

Improve the physical and biological conditions of 

the stream to enhance the intolerant fishery and to 

meet the current biological use designation.

2. Protect endangered fish species.

3. Maintain recreational uses.

4. Protect and (or) enhance the quality of water 

delivered to the Sheboygan River.

5. Improve wildlife habitat.

Preliminary pollutant-reduction goals to help achieve 

these objectives were set at a 75-percent reduction of 

sediment loads and a 50-percent reduction of phosphorus 

loads. Data resulting from this project indicate that the 

water quality and habitat are improving, but detectable 

improvements in the fish populations were not observed. 

Estimates of the rainfall storm load reductions (tables 4 

and 5), reductions in base-flow concentrations (table 2), 

and improvements in stream habitat (table 6) indicate that 

stream conditions overall have improved. Estimates of 

rainfall storm load reductions indicate that preliminary 

objectives set forth by the WDNR were realistic and that 
24 Effects of Best-Management Practices in Otter Creek in the Sheboygan River Priority Watershed, Wisconsin, 1990–2002

the final reductions came close to achieving these objectives. The level of BMP implementation was high for all 

types of targeted areas except upland BMPs and stream 

crossings. Considering that an estimated 97 percent of the 

total suspended solids that reaches Otter Creek originates 

from eroding cropland (Wisconsin Department of Natural 

Resources, 1993), additional upland BMP implementation 

could possibly reduce pollutant loads substantially more. 

In comparison to specific objectives of the Nonpoint 

Source Control Plan, the success of the project in meeting 

each individual objective varied. Specific objectives are 

addressed as follows:

1. The current forage-fishery classification and 

biological use designation was maintained. Habitat 

was improved, but the intolerant fishery was not 

enhanced as measured by the number of intolerant 

species present. 

2. Sampling during the course of the project did not 

show that the endangered species identified in the 

Nonpoint Source Control Plan (the striped shiner) 

was present at any of the sampling stations before 

or after installation of BMPs. A few of these species were identified at a sampling station in 1987 

downstream from all of the sampling stations for 

this study. The 1987 sampling station was within 

less than 1,000 feet of the Sheboygan River. This 

sampling event was the reason that the nonpoint 

source control plan specifically identified the 

striped shiner as being resident in Otter Creek, but 

it has not been identified there since. 

3. Recreational use was classified as partial body 

contact in the Nonpoint Source Control Plan, and 

this has not changed throughout the study period. 

Fishable numbers of warm water sport fish were 

not present before BMP implementation or during 

the post-BMP period.

4. The quality of water delivered to the Sheboygan River was shown to be improved except for 

the increase in fecal coliform concentrations, as 

shown by a decrease in concentrations of total 

suspended solids and BOD 5

 in base flow and a 

decrease in storm loads of total suspended solids, 

total phosphorus, and dissolved ammonia nitrogen 

from rainfall periods.

5. Habitat in the stream and riparian areas was 

improved.

In general, those objectives concerning water quality 

and habitat were met, and some of those concerning the 

Otter Creek fishery were met, but improvements in the fish 

communities were not observed.

Summary and Conclusions

The U.S. Geological Survey and the Wisconsin 

Department of Natural Resources began a comprehensive, 

multidisciplinary evaluation-monitoring program in 1989 

to assess the effectiveness of best-management practices 

(BMPs) funded through the Wisconsin Nonpoint Source 

Program. Hydrologic, water-quality, habitat, and fish data 

were collected at Otter Creek from 1990 to 2002 with the 

pre-BMP period ending in September 1993 and the postBMP period beginning in October 1999. BMPs installed 

in this watershed included streambank protection and 

fencing, stream crossings, grade stabilization, buffer strips, 

various barnyard-runoff controls, nutrient management, 

and a small amount of upland BMPs.

Water-quality samples were collected during base 

flow for the entire study period and during storms for two 

periods, pre- and post-BMP implementation. Base-flow 

samples were analyzed for total suspended solids, total 

phosphorus, dissolved ammonia nitrogen, BOD5

, and fecal 

coliform. Storm samples were analyzed for total suspended 

solids, total phosphorus, and dissolved ammonia nitrogen. 

Statistically significant differences between pre- and postBMP periods were detected in median concentrations of 

total suspended solids and BOD5 in base-flow samples but 

not total phosphorus or dissolved ammonia nitrogen; fecal 

coliform concentrations increased over the study period.

The median storm loads for total suspended solids, 

total phosphorus, and dissolved ammonia nitrogen during 

rainfall periods were compared statistically by means of 

the Wilcoxon rank-sum test. This test was also applied 

to regression residuals to test for differences between the 

pre- and post-BMP periods. Regression equations were 

constructed to remove some of the variability due to natural factors; a difference in the regression residuals is more 

likely to indicate a difference in water quality due to the 

BMPs than a test of differences using the raw storm-load 

data would have indicated.

Differences between the pre- and post-BMP storm 

loads from rainfall periods during the nonvegetative 

season were statistically significant at the 0.05 level for all 

three constituents monitored, as determined by changes 

in storm-load residuals from the regression equations. 

Although median storm loads from rainfall periods for 
References Cited 25

the nonvegetative season were less during the post-BMP 

period than during the pre-BMP period, differences in 

storm-load residuals for this period did not prove to be 

statistically significant. When considering data from the 

entire year, changes in storm-load residuals were significant for two of the three water-quality constituents (total 

suspended solids and dissolved ammonia nitrogen).

The results from analysis of storm loads from rainfall 

periods suggest that the installation of BMPs was effective 

at reducing pollutant loads during the nonvegetative season, but conclusions could not be made about results from 

the vegetative season. This is not necessarily an indication 

that the BMPs are not effective during the vegetative season, but is more likely to be an artifact of the climatic and 

land-cover conditions during this period of the year.

Habitat and fish data were collected between July 

30 and September 11 each year of the study to track the 

effects of BMPs on stream habitat and fish communities. 

Various habitat and fish characteristics were sampled or 

measured. These characteristics were used as variables to 

compute habitat-quality index scores and an index of biotic 

integrity (IBI). Final trend analysis using ANCOVA was 

done on the index scores, as well as some of the original 

variables to explore changes due to BMP implementation. 

Variability in both habitat and fish data was considerable. 

Habitat was improved for stream segments that had either 

natural riparian buffer or had streambank fencing installed, 

but not at the station where the riparian area was pasture 

and no streambank fencing was installed. The results also 

suggest that BMP implementation in Otter Creek substantially modified fish community structure, but the overall 

community quality represented by IBI and percentage of 

intolerant individuals was not improved. 

Acknowledgments

Support for this study included contributions from 

the Wisconsin Department of Natural Resources, the U.S. 

Environmental Protection Agency, and the U.S. Geological Survey. The authors thank the staff at the Sheboygan 

County Land and Water Conservation Department who 

provided land-use data, communication with land owners, 

and input on the interpretation of final results. The authors 

also thank Troy Rutter and other colleagues at the U.S. 

Geological Survey and Wisconsin Department of Natural 

Resources for their work throughout the project.

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