The Milwaukee Metropolitan Sewerage District (MMSD) Corridor Study is a three-phase project designed to improve the understanding of water resources in the MMSD planning area to assist managers and policy makers in their decisions. Phase I of the Study involved the compilation of existing data from multiple agencies into a single database. These data were analyzed to identify spatial, temporal, and technological gaps in the planning area, and were used to develop Phase II of the Study. Phase II, the subject of this report, involved an intensive data-collection effort by the U.S. Geological Survey (USGS) in cooperation with MMSD (from February, 2004, through September, 2005). This phase addressed the data gaps identified in Phase I and completed a baseline assessment of water quality for selected stream and harbor sites in the MMSD planning area. This baseline assessment included evaluations of surface-water chemistry and microbial concentrations in the streams and harbor sites; additionally, stream sites were evaluated for discharge, sediment chemistry, fish-tissue chemistry, habitat, and the quality of biological communities (including fish, macroinvertebrates, and algae). In all, data were collected at 15 stream and 6 harbor sites within the MMSD planning area, including manual sampling and analysis for more than 220 water-quality properties and constituents at all 21 sites, stream-discharge data for 14 stream sites, and automated water-quality sampling at 4 stream sites. A bioassessment during autumn 2004 included collection of biologic-community data and stream-habitat data at wadeable streams. Quartiles of Phase II aggregate bioassessment rankings were used to divide the 14 wadeable stream sites into four groups to investigate relations between bioassessment data and site characteristic and water-quality data. Quartile numbers reflect relative water quality: quartile 1 contained sites where the bioassessment data indicated the least-degraded water quality among those sampled, and quartile 4 contained sites that indicated the most-degraded water quality. Quartiles contained the following stream sites: Quartile 1: Milwaukee River near Cedarburg, Milwaukee River at Milwaukee, Jewel Creek, and Menomonee River at Menomonee Falls; Quartile 2: Willow Creek, Root River near Franklin, and Root River at Grange Avenue; Quartile 3: Menomonee River at Wauwatosa, Oak Creek, and Little Menomonee River; and Quartile 4: Honey Creek, Underwood Creek, Lincoln Creek, and Kinnickinnic River. Site characteristics (in this case, drainage area and land use) and selected water-quality data were summarized based on the four bioassessment quartiles to determine if there were relations with the aggregate bioassessment rankings. In general, sites having the largest drainage basins with the lowest proportion of urban land use were in quartile 1, and the smallest drainage basins with the highest proportion of urban land use were in quartile 4. Major ions, indicator organisms, and wastewater compounds generally had the lowest overall results in quartile 1 and highest overall results in quartile 4, with intermediate results in quartiles 2 and 3. Results for other constituent types (nutrients, mercury, pathogenic organisms, and bed sediment) were mixed, with results for some constituents decreasing from quartile 1 to quartile 4. Where sufficient Phase I data were available, summary statistics (including medians) for chemical and biological data were calculated, allowing some comparisons to be made between Phase I and Phase II data. Comparisons between Phase I and Phase II results indicated a variety of changes with respect to water quality. Concentrations of chloride, nitrate, chlorophyll a, total phosphorus in water; arsenic in bed sediment; and fish Index of Biotic Integrity ratings generally indicated declines in water quality. However, concentrations of total nitrogen, suspended sediment, and fecal coliform in water; some trace eleme