The transport and biological effects of dormant spray pesticides were examined in the San Francisco Estuary, California, by measuring dissolved- pesticide concentrations and estimating toxicity using bioassays at a series of sites in January and February 1993. Distinct pulses of pesticides, including diazinon, methidathion, and chlorpyrifos, were detected in the San Joaquin River in January and February and in the Sacramento River in February following rainfall. The higher pesticide loads in the Sacramento River compared with those in the San Joaquin River can be attributed to the greater amount of rainfall in the Sacramento Valley. The use patterns and water solubility of the pesticides can account for the observed temporal and spatial distributions in the two rivers. The pesticide pulses detected at Sacramento were followed through the northern embayment of San Francisco Estuary. In contrast, the pesticide distribution in the Sacramento-San Joaquin Delta changed from distinct pulses to steady increases in concentration over time. Seven-day bioassays indicated that Sacramento River water at Rio Vista was acutely toxic to Ceriodaphnia dubia (water flea) for 3 consecutive d and San Joaquin River water at Vernalis for 12 consecutive d. These water samples all had the highest diazinon concentrations. Examination of 96-h LC50 values (lethal concentration that kills 50% of test organisms in 96 H) indicates that measured diazinon concentrations could account for most but not all the observed toxicity. Other pesticides present could contribute to the toxicity.