Cholinesterase (ChE) enzyme activity measurements are widely applied in aquatic organisms for water quality monitoring, especially for pesticide contamination in agricultural watersheds. These biomarkers are amenable to measurement in a variety of species, and are therefore useful for examining effects in model organisms relevant to the ecosystem of interest. However, extensive variation in ChE biochemistry exists among tissues and species. This variation is rarely characterized and may lead to biases in the interpretation of activity determinations. We optimized ChE activity measurement parameters and characterized ChE biochemistry in Sacramento sucker (Catostomus occidentalis), a widely distributed fish native to watersheds of the Central Valley of California. Acetylcholinesterase (AChE) was the predominant ChE present in C. occidentalis brain and muscle, and muscle AChE was most sensitive to diazinon inhibition. Field caging experiments indicated that exposures to ChE-inhibiting pesticides were insufficient to induce neurotoxic effects. However, pesticide usage in the Central Valley is highly variable among years, and long-term monitoring of in-stream effects would be necessary to evaluate trends in pesticide contamination. Recent changes to the State Water Code require agricultural landowners to participate in a regional water quality monitoring plan. As with most regional monitoring plans, measurements of in-stream effects, and effects in resident species, are not scheduled to be included. We suggest that inclusion of biomarker measures would lend important information to the monitoring process, and propose these procedures as a template for adapting ChE activity measurements into region-specific monitoring programs to assess in-stream effects of pesticide contamination on native species.