Inputs to the Yolo Bypass are potential sources of pesticides that could impact critical life stages of native fish. To assess the direct inputs during inundation, pesticide concentrations were analyzed in water, in suspended and bed-sediment samples collected from six source watersheds to the Yolo Bypass, and from three sites within the Bypass in 2004 and 2005. Water samples were collected in February 2004 from the six input sites to the Bypass during the first flood event of the year representing pesticide inputs during high-flow events. Samples were also collected along a transect across the Bypass in early March 2004 and from three sites within the Bypass in the spring of 2004 under low-flow conditions. Low-flow data were used to understand potential pesticide contamination and its effects on native fish if water from these areas were used to flood the Bypass in dry years. To assess loads of pesticides to the Bypass associated with suspended sediments, large-volume water samples were collected during high flows in 2004 and 2005 from three sites, whereas bed sediments were collected from six sites in the fall of 2004 during the dry season. Thirteen current-use pesticides were detected in surface water samples collected during the study. The highest pesticide concentrations detected at the input sites to the Bypass corresponded to the first high-flow event of the year. The highest pesticide concentrations at the two sites sampled within the Bypass during the early spring were detected in mid-April following a major flood event as the water began to subside. The pesticides detected and their concentrations in the surface waters varied by site; however, hexazinone and simazine were detected at all sites and at some of the highest concentrations. Thirteen current-use pesticides and three organochlorine insecticides were detected in bed and suspended sediments collected in 2004 and 2005. The pesticides detected and their concentrations varied by site and sediment sample type. Trifluralin, p,p'-DDE, and p,p'-DDT were highest in the bed sediments, whereas oxyfluorfen and thiobencarb were highest in the suspended sediments. With the exception of the three organochlorine insecticides, suspended sediments had higher pesticide concentrations compared with bed sediments, indicating the potential for pesticide transport throughout the Bypass, especially during high-flow events. Understanding the distribution of pesticides between the water and sediment is needed to assess fate and transport within the Bypass and to evaluate the potential effects on native fish.