An assessment of organic chemicals and aquatic toxicity in streams located near Milwaukee, Wisconsin, indicated high potential for adverse impacts on aquatic organisms that could be related to organic waste compounds (OWCs). OWCs used in agriculture, industry, and households make their way into surface waters through runoff, leaking septic-conveyance systems, regulated and unregulated discharges, and combined sewage overflows, among other sources. Many of these compounds are toxic at elevated concentrations and (or) known to have endocrine-disrupting potential, and often they occur as complex mixtures. There is still much to be learned about the chronic exposure effects of these compounds on aquatic populations. During 2006–9, the U.S. Geological Survey, in cooperation with the Milwaukee Metropolitan Sewerage District (MMSD), conducted a study to determine the occurrence and potential toxicity of OWCs in different stream compartments and flow regimes for streams in the Milwaukee area. Samples were collected at 17 sites and analyzed for a suite of 69 OWCs. Three types of stream compartments were represented: water column, streambed pore water, and streambed sediment. Water-column samples were subdivided by flow regime into stormflow and base-flow samples. One or more compounds were detected in all 196 samples collected, and 64 of the 69 compounds were detected at least once. Base-flow samples had the lowest detection rates, with a median of 12 compounds detected per sample. Median detection rates for stormflow, pore-water, and sediment samples were more than double that of base-flow samples. Compounds with the highest detection rates include polycyclic aromatic hydrocarbons (PAHs), insecticides, herbicides, and dyes/pigments. Elevated occurrence and concentrations of some compounds were detected in samples from urban sites, as compared with more rural sites, especially during stormflow conditions. These include the PAHs and the domestic waste-water-indicator compounds, among others. Urban runoff and storm-related leaks of sanitary sewers and (or) septic systems may be important sources of these and other compounds to the streams. The Kinnickinnic River, a highly urbanized site, had the highest detection rates and concentrations of compounds of all the sampled sites. The Milwaukee River near Cedarburg—one of the least urban sites—and the Outer Milwaukee Harbor site had the lowest detection rates and concentrations. Aquatic-toxicity benchmarks were exceeded for 12 of the 25 compounds with known benchmarks. The compounds with the greatest benchmark exceedances were the PAHs, both in terms of exceedance frequency (up to 93 percent for some compounds in sediment samples) and magnitude (concentrations up to 1,024 times greater than the benchmark value). Other compounds with toxicity-benchmark exceedances include Bis(2-ethylhexyl) phthalate (a plasticizer), 2-Methylnapthalene (a component of fuel and oil), phenol (an antimicrobial disinfectant with diverse uses), and 4-Nonylphenol (sum of all isomers; a detergent metabolite, among other uses). Analyzed as a mixture, the suite of PAH compounds were found to be potentially toxic for most non-base-flow samples. Bioassay tests were conducted on samples from 14 streams: Ceriodaphnia dubia in base-flow samples, Ceriodaphnia dubia and Hyallela azteca in pore-water samples, and Hyallela azteca and Chironomus tentans in sediment samples. The greatest adverse effect was observed in tests with Chironomus tentans from sediment samples. The weight of Chironomus tentans after exposure to sediments decreased with increased OWC concentrations. This was most evident in the relation between PAH results and Chironomus tentans bioassay results for the majority of samples; however, solvents and flame retardants appeared to be important for one site each. These results for PAHs were consistent with assessment of PAH potency factors for sediment, indicating that PAHs were likely to have adverse effects on aquatic organisms in many of the streams studied.