The Salinas Valley in Monterey County, California, USA, is a highly productive agricultural region. Irrigation runoff containing pesticides at concentrations toxic to aquatic organisms poses a threat to aquatic ecosystems within local watersheds. This study monitored the effectiveness of a constructed wetland treatment system with a granulated activated carbon (GAC) filter installation at reducing pesticide concentrations and associated toxicity to Ceriodaphnia dubia, Hyalella azteca, and Chironomus dilutus. The wetland was supplied with water pumped from an impaired agricultural and urban drainage. Across five monitoring trials, the integrated system’s average pesticide concentration reduction was 52%. The wetland channel and GAC filtration components individually provided significant treatment, and within each, pesticide solubility had a significant effect on changes in pesticide concentrations. The integrated treatment system also reduced nitrate by 61%, phosphate by 73%, and turbidity by 90%. Input water was significantly toxic to C. dubia and H. azteca in the first trial. Toxicity to C. dubia persisted throughout the system, whereas toxicity to H. azteca was removed by the channel, but there was residual toxicity post-GAC. The final trial had significant input toxicity to H. azteca and C. dilutus. The channel reduced toxicity to H. azteca and removed toxicity to C. dilutus. GAC filtration reduced H. azteca toxicity to an insignificant level. There was no input toxicity in the other three trials. The results demonstrate that a wetland treatment system coupled with GAC filtration can reduce pesticide concentrations, nutrients, suspended particles, and aquatic toxicity associated with agricultural runoff.