Single-species toxicity testing of ambient water samples and national-scale probabilistic risk assessment have implicated the organophosphorous (OP) insecticide chlorpyrifos (O, O-diethyl O-(3,5,6-trichloro-2-pyridyl)-phosphorothioate) as a potential chemical stressor of aquatic organisms residing in the lower San Joaquin River basin. This site-specific aquatic ecological risk assessment was conducted to determine the probability of adverse effects occurring from exposure to chlorpyrifos in an agriculturally dominated tributary of the San Joaquin River and to assess the ecological significance of such effects. Assessment endpoints were fish population persistence and invertebrate community productivity. Daily chemical measurements collected over a period of one year were analyzed temporally for frequency, duration, and spacing between events for acute and chronic exposure episodes. Effects thresholds for fish and freshwater lotic invertebrates were determined from single-species laboratory toxicity tests. Potential risk was characterized by the degree of overlap of distributions of exposure events and effects, with consideration given to additive toxicity of other OP insecticides, recovery periods, and duration of chronic exposure (≥ 21 d). Ecological significance was determined by analysis of fish assemblage dietary and reproductive habits in relation to the surrogate invertebrate taxa judged at risk. Results of analysis indicated no direct effects on fish, and indirect effects on fish through elimination of invertebrate food items were considered unlikely. Biological survey information will be necessary to address uncertainty in this risk conclusion, especially as it relates to the benthic invertebrate community. Results of this site-specific risk analysis suggest that fish population persistence and invertebrate community productivity were not adversely affected by measured chlorpyrifos residues during a year-long monitoring period.