Introduction
Purpose and Scope
Study Design, Sample Collection, and Results of Quality Assurance
Land Use and Phase II Sites
Collection of Stage and Discharge Data
Manual Water-Quality Sampling
Mercury Sampling
Microbiological Sampling
Bed-Sediment Sampling
Water-Column-Toxicity Sampling
Biological, Habitat Assessment, and Fish-Tissue Toxicity Sampling
Semipermeable Membrane Device Sampling from the National Water-Quality Assessment Program
Automated Water-Quality Sampling
Quality Assurance and Quality Control
Special Cases of Quality Control for Selected Constituents
Evaluation of Data Collected During Phase II
Hydrologic Conditions During the Study Period
Precipitation
Discharge and Runoff
Results from Manually and Automatically Collected Samples
Chloride
Loads, Yields, and Volumetrically Weighted Concentrations of Chloride
Nutrients and Chlorophyll a
Total Nitrogen
Nitrate
Total Phosphorus
Loads, Yields, and Volumetrically Weighted Concentrations of Total Phosphorus
Chlorophyll a
Suspended Sediment
Loads, Yields, and Volumetrically Weighted Concentrations of Suspended Sediment
Mercury
Total Mercury
Methylmercury
Indicator Organisms
Fecal Coliforms
Escherichia coli
Coliphage
Groups II and III
Pathogenic Organisms
Escherichia coli O157:H7
Salmonella
Detection frequencies
Concentrations
Giardia
Detection frequencies
Concentrations
Cryptosporidium
Detection frequencies
Concentrations
Pesticides
Wastewater Compounds
Detection Frequencies
Response to Flow and Seasonality
Dominant Constituents in Wastewater Compound Classes
Endocrine-Disrupting Chemicals
Semipermeable Membrane Devices and Wastewater Compounds
Bed Sediment
Physical Characteristics of Sediment-Trap Contents
Comparison of Sites by Use of Average Effect Concentrations
Comparison of Sites by Use of Individual Contaminant Effects Concentrations
Comparison of Sites by Use of Total Phosphorus Enrichment
Water-Column Toxicity
Fish Tissues
Bioassessment
Fish Results
Macroinvertebrate Results
Algae Results
Relations among Habitat Variables and Biotic Communities
Relations between Stream Biological Metrics, Site Characteristics, and Water-Quality Data
Potential Areas for Data Collection in Phase III
Summary
Summary of Relations between Biological Metrics, Site Characteristics, and Water-Quality Data
Findings for Harbor Sites and the Milwaukee River at Mouth at Milwaukee Site
Phase I–Phase II Comparisons
References
Appendixes

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Figures

Figure 1. Map showing locations of sites sampled during Phase II in the Milwaukee Metropolitan Sewerage District planning area, Wis.

Figure 2. Map showing land use/land cover and stream-site drainage-area boundaries for stream sites sampled during Phase II of the Milwaukee Metropolitan Sewerage District Corridor Study.

Figure 3. Graph showing land use for Phase II sites of the Milwaukee Metropolitan Sewerage District Corridor Study.

Figure 4. Map showing locations and characteristics of Phase II sampling sites, and locations of National Weather Service precipitation gages in the Milwaukee Metropolitan Sewerage District planning area, Wis.

Figure 5. Chart showing timeline of data-collection activities for Phase II of the Milwaukee Metropolitan Sewerage District Corridor Study.

Figure 6. Photograph showing sediment traps used for collection of bed-sediment samples during Phase II of the Milwaukee Metropolitan Sewerage District Corridor Study.

Figure 7. Graph showing inter-laboratory correlation between Phase II results for A, fecal coliform concentrations, and B, Escherichia coli concentrations from samples analyzed at the Wisconsin State Laboratory of Hygiene and Milwaukee Metropolitan Sewerage District.

Figure 8. Graph showing distribution of chloride concentrations, by site, in the Milwaukee Metropolitan Sewerage District planning area, Wis.

Figure 9. Graph showing median chloride concentrations plotted against percent urban land use in drainage basins for 15 stream sites in the Milwaukee Metropolitan Sewerage District planning area, Wis.

Figure 10. Graph showing distributions of chloride concentrations for stream and harbor samples, Milwaukee Metropolitan Sewerage District planning area, Wis.

Figure 11. Graph showing distribution of total nitrogen concentrations, by site, in the Milwaukee Metropolitan Sewerage District planning area, Wis.

Figure 12. Graph showing distributions of total nitrogen concentrations for stream and harbor samples, Milwaukee Metropolitan Sewerage District planning area, Wis.

Figure 13. Map showing Phase I and Phase II comparison of median total nitrogen concentrations in the Milwaukee Metropolitan Sewerage District planning area, Wis.

Figure 14. Graph showing distribution of nitrate concentrations, by site, in the Milwaukee Metropolitan Sewerage District planning area, Wis.

Figure 15. Graph showing distributions of nitrate concentrations for stream and harbor samples, Milwaukee Metropolitan Sewerage District planning area, Wis.

Figure 16. Map showing Phase I and Phase II comparison of median nitrate concentrations in the Milwaukee Metropolitan Sewerage District planning area, Wis.

Figure 17. Graph showing distribution of total phosphorus concentrations, by site, in the Milwaukee Metropolitan Sewerage District planning area, Wis.

Figure 18. Graph showing distributions of total phosphorus concentrations for stream and harbor samples, Milwaukee Metropolitan Sewerage District planning area, Wis.

Figure 19. Map showing Phase I and Phase II comparison of median total phosphorus concentrations in the Milwaukee Metropolitan Sewerage District planning area, Wis.

Figure 20. Graph showing distribution of chlorophyll a concentrations, by site, in the Milwaukee Metropolitan Sewerage District planning area, Wis.

Figure 21. Graph showing distributions of chlorophyll a concentrations for stream and harbor samples, Milwaukee Metropolitan Sewerage District planning area, Wis.

Figure 22. Graph showing distribution of suspended-sediment concentrations, by site, in the Milwaukee Metropolitan Sewerage District planning area, Wis.

Figure 23. Graph showing distributions of suspended-sediment concentrations for stream and harbor samples, Milwaukee Metropolitan Sewerage District planning area, Wis.

Figure 24. Graph showing median dissolved total mercury concentrations plotted against percent urban land use in site drainage basins for 15 stream sites in the Milwaukee Metropolitan Sewerage District planning area, Wis.

Figure 25. Graph showing median concentrations of total mercury, by site, in the Milwaukee Metropolitan Sewerage District planning area, Wis.

Figure 26. Graph showing median concentrations of methylmercury, by site, in the Milwaukee Metropolitan Sewerage District planning area, Wis.

Figure 27. Graph showing median concentrations of fecal coliform plotted against percent urban land use in site drainage basins for 15 stream sites in the Milwaukee Metropolitan Sewerage District planning area, Wis.

Figure 28. Graph showing distribution of fecal coliform concentrations, by site, in the Milwaukee Metropolitan Sewerage District planning area, Wis.

Figure 29. Graph showing distributions of fecal coliform concentrations for stream and harbor sites, Milwaukee Metropolitan Sewerage District planning area, Wis.

Figure 30. Graph showing median concentrations of E. coli plotted against percent urban land use in site drainage basins for 15 stream sites in the Milwaukee Metropolitan Sewerage District planning area, Wis.

Figure 31. Graph showing distribution of E. coli concentrations, by site, in the Milwaukee Metropolitan Sewerage District planning area, Wis.

Figure 32. Graph showing distributions of E. coli concentrations for stream and harbor sites, Milwaukee Metropolitan Sewerage District planning area, Wis.

Figure 33. Graph showing median concentrations of coliphage plotted against percent urban land use in site drainage basins for 15 stream sites in the Milwaukee Metropolitan Sewerage District planning area, Wis.

Figure 34. Graph showing distribution of coliphage concentrations, by site, in the Milwaukee Metropolitan Sewerage District planning area, Wis.

Figure 35. Graph showing distributions of coliphage concentrations for stream and harbor sites, Milwaukee Metropolitan Sewerage District planning area, Wis.

Figure 36. Graph showing detection frequency of coliphage groups II and (or) III in samples, by site, in the Milwaukee Metropolitan Sewerage District planning area, Wis.

Figure 37. Graph showing detection frequencies of coliphage groups II and (or) III detections for stream and harbor sites, Milwaukee Metropolitan Sewerage District planning area, Wis.

Figure 38. Graph showing detection frequencies and concentrations of Salmonella in samples, by site, in the Milwaukee Metropolitan Sewerage District planning area, Wis.

Figure 39. Graph showing detection frequencies and concentrations of Salmonella for stream sites, Milwaukee Metropolitan Sewerage District planning area, Wis.

Figure 40. Graph showing detection frequencies and concentrations of Giardia in samples by site in the Milwaukee Metropolitan Sewerage District planning area, Wis.

Figure 41. Graph showing detection frequencies and concentrations of Giardia for stream and harbor sites, Milwaukee Metropolitan Sewerage District planning area, Wis.

Figure 42. Graph showing detection frequencies and concentrations of Cryptosporidium in samples, by site, in the Milwaukee Metropolitan Sewerage District planning area, Wis.

Figure 43. Graph showing detection frequencies and concentrations of Cryptosporidium for stream and harbor sites, Milwaukee Metropolitan Sewerage District planning area, Wis.

Figure 44. Graph showing detection frequencies of selected classes of Group 1 wastewater compounds (polycyclic aromatic hydrocarbons, antioxidants, plasticizers, dyes and pigments, and fire retardants), by site, in the Milwaukee Metropolitan Sewerage District planning area, Wis.

Figure 45. Graph showing detection frequencies of Group 2 solvent and fuel wastewater-compound classes, by site, in the Milwaukee Metropolitan Sewerage District planning area, Wis.

Figure 46. Graph showing detection frequencies of Group 3 insecticide and herbicide wastewater-compound classes, by site, in the Milwaukee Metropolitan Sewerage District planning area, Wis.

Figure 47. Graph showing detection frequencies of selected classes of Group 4 wastewater compounds (flavors and fragrances, nonprescription human drugs, antimicrobial disinfectants, detergent metabolites, and sterols), by site, in the Milwaukee Metropolitan Sewerage District planning area, Wis.

Figure 48. Graph showing detection frequency of stream samples with wastewater-compound detections during high-and low-flow periods, by WWC class, in the Milwaukee Metropolitan Sewerage District planning area, Wis.

Figure 49. Graph showing detection frequency of stream samples with wastewater-compound detections, by season and WWC class, in the Milwaukee Metropolitan Sewerage District planning area, Wis.

Figure 50. Graph showing detection frequency of stream samples with wastewater-compound detections during low-flow periods, by season and WWC class, in the Milwaukee Metropolitan Sewerage District planning area, Wis.

Figure 51. Graph showing detection frequency of stream samples with wastewater-compound detections during high-flow periods, by season and WWC class, in the Milwaukee Metropolitan Sewerage District planning area, Wis.

Figure 52. Graph showing detection frequency of harbor samples with wastewater-compound detections, by season and WWC class, in the Milwaukee Metropolitan Sewerage District planning area, Wis.

Figure 53. Map showing distribution and frequency of known and suspected endocrine-disrupting compounds in the Milwaukee Metropolitan Sewerage District planning area, Wis.

Figure 54. Graph showing mass and particle-size distribution of sediment captured in Phase II sediment traps in the Milwaukee Metropolitan Sewerage District planning area, Wis.

Figure 55. Graph showing particle-size distribution in sediment-trap samples, by Phase II sampling location, in the Milwaukee Metropolitan Sewerage District planning area, Wis.

Figure 56. Graph showing number of consensus-based threshold effect concentration exceedences and the mean consensus-based probable effects concentration quotients for contaminants in sediments from the Milwaukee Metropolitan Sewerage District planning area, Wis.

Figure 57. Graph showing consensus-based probable effects concentration quotients for nine contaminants in the Milwaukee Metropolitan Sewerage District planning area, Wis.

Figure 58. Graph showing total phosphorus enrichment factor relative to background upland soil concentrations in the Milwaukee Metropolitan Sewerage District planning area, Wis.

Figure 59. Graph showing Fish Index of Biotic Integrity scores plotted against percent urban land use in site drainage basins for 15 stream sites in the Milwaukee Metropolitan Sewerage District planning area, Wis.

Figure 60. Map showing sites sampled for macroinvertebrates with percent Ephemeroptera, Plecoptera, and Trichoptera taxa in the Milwaukee Metropolitan Sewerage District planning area, Wis.

Figure 61. Graph showing percent Ephemeroptera, Plecoptera, and Trichoptera taxa plotted against percent urban land use in site drainage basins for 15 stream sites in the Milwaukee Metropolitan Sewerage District planning area, Wis.

Figure 62. Map showing sites sampled for macroinvertebrates with Hilsenhoff Biotic Index in the Milwaukee Metropolitan Sewerage District planning area, Wis.

Figure 63. Graph showing a modified Hilsenhoff Biotic Index (HBI-10) plotted against percent urban land use in site drainage basins for 15 stream sites in the Milwaukee Metropolitan Sewerage District planning area, Wis.

Figure 64. Graph showing percentage of diatoms in pollution-tolerance classes in the Milwaukee Metropolitan Sewerage District planning area, Wis.

Figure 65. Graph showing percent pollution-sensitive diatoms plotted against percent urban land use in site drainage basins for 15 stream sites in the Milwaukee Metropolitan Sewerage District planning area, Wis.

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Table 1A. Basin characteristics and streamflow statistics for stream sites sampled during Phase II of the Milwaukee Metropolitan Sewerage District Corridor Study.

Table 1B. Harbor sites sampled during Phase II of the Milwaukee Metropolitan Sewerage District Corridor Study.

Table 2. List of properties and constituents analyzed during Phase II of the Milwaukee Metropolitan Sewerage District Corridor Study.

Table 3. Results of constituent detections in field blanks during Phase II of the Milwaukee Metropolitan Sewerage District Corridor Study.

Table 4. Results of replicated sample issues during Phase II of the Milwaukee Metropolitan Sewerage District Corridor Study.

Table 5. Replicate results for indicator organisms analyzed by Wisconsin State Laboratory of Hygiene during Phase II of the Milwaukee Metropolitan Sewerage District Corridor Study.

Table 6. Replicate results for pathogenic organisms during Phase II of the Milwaukee Metropolitan Sewerage District Corridor Study.

Table 7. Relative percent differences in sediment-trap results for six sites in Phase II of the Milwaukee Metropolitan Sewerage District Corridor Study.

Table 8. Comparison of the Phase I subwatersheds to Phase II sites of the Milwaukee Metropolitan Sewerage District Corridor Study.

Table 9. Monthly and water-year totals for rain gages in the Milwaukee Metropolitan Sewerage District planning area, Wis.

Table 10. Median results for field measurements, major inorganics, and alkalinity that did not indicate any unusual water-quality patterns.

Table 11. Annual chloride load and yield, average daily chloride yield, total water flow, and volumetric total chloride concentrations for four Phase II sites in the Milwaukee Metropolitan Sewerage District planning area, Wis.

Table 12. Monthly and annual chloride loads for four Phase II sites in the Milwaukee Metropolitan Sewerage District planning area, Wis., for water years 2004 and 2005.

Table 13. Estimated nutrient concentrations in reference streams for the area encompassing the Milwaukee Metropolitan Sewerage District planning area, Wis.

Table 14. Annual total phosphorus load and yield, average daily phosphorus yield, total water flow, and volumetric total phosphorus concentrations for four Phase II sites in the Milwaukee Metropolitan Sewerage District planning area, Wis.

Table 15. Monthly and annual total phosphorus loads for four Phase II sites in the Milwaukee Metropolitan Sewerage District planning area, Wis., for water years 2004 and 2005.

Table 16. Annual suspended-sediment load and yield, average daily sediment yield, total water flow, and volumetrically weighted sediment concentrations for four Phase II sites in the Milwaukee Metropolitan Sewerage District planning area, Wis.

Table 17. Monthly and annual suspended-sediment loads for four Phase II sites in the Milwaukee Metropolitan Sewerage District planning area, Wis., for water years 2004 and 2005.

Table 18. Summary of detections and nondetections of wastewater compounds at all Phase II sites in the Milwaukee Metropolitan Sewerage District planning area, Wis.

Table 19. Grouping of wastewater-compound classes for Phase II of the Milwaukee Metropolitan Sewerage District Corridor Study.

Table 20. Summary of analtyical results of stream and harbor sites sampled for wastewater compounds during Phase II of the Milwaukee Metropolitan Sewerage District Corridor Study.

Table 21. Detection frequencies for Phase II wastewater compounds analysis in the Milwaukee Metropolitan Sewerage District planning area, Wis.

Table 22. Results for toxicity tests and selected chemical analyses of semi-permeable membrane device extracts and detection frequencies for Phase II wastewater-compounds analysis at seven sites in the Milwaukee Metropolitan Sewerage District.

Table 23. Maximum total polychlorinated biphenyl concentrations in sediment-trap samples for 15 Phase II stream sites collected during two surveys of the Milwaukee Metropolitan Sewerage District Corridor Study.

Table 24. Percent effects in samples with readings at or above 20 percent for all Phase II sites in the Milwaukee Metropolitan Sewerage District planning area, Wis.

Table 25. Summary of chemical analysis of whole fish at three Phase II stream sites of the Milwaukee Metropolitan Sewerage District Corridor Study, during one-time surveys conducted in October, 2004.

Table 26. Biotic integrity ratings for Index of Biotic Integrity score.

Table 27. Fish-community information from one-time surveys conducted during July, August, and October 2004, for 14 Phase II stream sites in the Milwaukee Metropolitan Sewerage District planning area, Wis.

Table 28. Water-quality ratings for Hilsenhoff Biotic Index and HBI-10 values.

Table 29. Macroinvertebrate community information from one-time surveys conducted during August and September 2004, for 14 Phase II stream sites in the Milwaukee Metropolitan Sewerage District planning area, Wis.

Table 30. Algal-community results from one-time surveys conducted in August and September 2004, for 14 Phase II stream sites in the Milwaukee Metropolitan Sewerage District planning area, Wis.

Table 31. Correlations among metrics of aquatic biology and selected habitat metrics for Phase II of the Milwaukee Metropolitan Sewerage District Corridor Study.

Table 32. Average trophic-level rankings and aggregate bioassessment rankings for Phase II stream sites in the Milwaukee Metropolitan Sewerage District planning area, Wis.

Table 33. Summarized results of Phase II constituents, grouped by aggregate bioassessment ranking in the Milwaukee Metropolitan Sewerage District planning area, Wis.

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Appendix 1. Land-use classes from Southeastern Wisconsin Regional Planning Commission and Wisconsin Department of Natural Resources WISCLAND land-cover data sets.

Appendix 2a–b. Descriptions of methods for harbor-site sampling and mercury sampling.

Appendix 3. Water-quality properties and constituents, reporting levels, and analyzing laboratories.

Appendix 4. Assignment of season and flow conditions, by site and by sampling event, for Phase II sampling in the Milwaukee Metropolitan Sewerage District planning area, Wisconsin, 2004–05.

Appendix 5. Comparison of median constituent concentrations and detections between Phase I and Phase II of the MMSD Corridor Study.

Appendix 6. Hydrologic conditions during Phase II of the Milwaukee Metropolitan Sewerage District Corridor Study.

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Conversion Factors and Abbreviations

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Other Abbreviations

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Acknowledgements

Technical Reviewers

Dale M. Robertson, Research Hydrologist (Chemistry), U.S. Geological Survey, Middleton, Wis.
Herbert S. Garn, Assistant Center Director, U.S. Geological Survey, Middleton, Wis.
Eric Waldmer, Water Resources/Aquatic Biology Supervisor, Milwaukee Metropolitan Sewerage District, Milwaukee, Wis.
Chris Magruder, Community and Environmental Liaison, Milwaukee Metropolitan Sewerage District, Milwaukee, Wis.

Editorial and Graphics

Michael Eberle, Technical Publications Editor, U.S. Geological Survey, Columbus, Ohio
S. Bridgett Marsh, Hydrologist, U.S. Geological Survey, Middleton, Wis.
Michelle Greenwood, Geographer, U.S. Geological Survey, Middleton, Wis.

Data Collection

Troy D. Rutter, Hydrologic Technician, U.S. Geological Survey, Middleton, Wis.
Krista A. Stensvold, Hydrologist, U.S. Geological Survey, Middleton, Wis.
Timothy L. Hanson, Hydrologic Technician, U.S. Geological Survey, Middleton, Wis.
U.S. Geological Survey and Milwaukee Metropolitan Sewerage District field and laboratory personnel

Approving Official

Dorothy H. Tepper, Northeast Region Reports Improvement Advisor, U.S. Geological Survey, Reston, Va.

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