This is the second part of a study that evaluates the influence of nonpoint sources on the sediment quality of five adjacent streams within the metropolitan Kansas City area, central United States. Physical, chemical, and toxicity data (Hyalella azteca 28-day whole-sediment toxicity test) for 29 samples collected in 2003 were used for this evaluation, and the potential causes for the toxic effects were explored. The sediments exhibited a low to moderate toxicity, with five samples identified as toxic to H. azteca. Metals did not likely cause the toxicity based on low concentrations of metals in the pore water and elevated concentrations of acid volatile sulfide in the sediments. Although individual polycyclic aromatic hydrocarbons (PAHs) frequently exceeded effect-based sediment quality guidelines [probable effect concentrations (PECs)], only four of the samples had a PEC quotient (PEC-Q) for total PAHs over 1.0 and only one of these four samples was identified as toxic. For the mean PEC-Q for organochlorine compounds (chlordane, dieldrin, sum DDEs), 4 of the 12 samples with a mean PEC-Q above 1.0 were toxic and 4 of the 8 samples with a mean PEC-Q above 3.0 were toxic. Additionally, four of eight samples were toxic, with a mean PEC-Q above 1.0 based on metals, PAHs, polychlorinated biphenyls (PCBs), and organochlorine pesticides. The increase in the incidence of toxicity with the increase in the mean PEC-Q based on organochlorine pesticides or based on metals, PAHs, PCBs, and organochlorine pesticides suggests that organochlorine pesticides might have contributed to the observed toxicity and that the use of a mean PEC-Q, rather than PEC-Qs for individual compounds, might be more informative in predicting toxic effects. Our study shows that stream sediments subject to predominant nonpoint sources contamination can be toxic and that many factors, including analysis of a full suite of PAHs and pesticides of both past and present urban applications and the origins of these organic compounds, are important to identify the causes of toxicity.