Watersheds of the Great Lakes Basin (USA/Canada) are highly modified and impacted by human activities including pesticide use. Despite labeling restrictions intended to minimize risks to nontarget organisms, concerns remain that environmental exposures to pesticides may be occurring at levels negatively impacting nontarget organisms. We used a combination of organismal-level toxicity estimates (in vivo aquatic life benchmarks) and data from high-throughput screening (HTS) assays (in vitro benchmarks) to prioritize pesticides and sites of concern in streams at 16 tributaries to the Great Lakes Basin. In vivo or in vitro benchmark values were exceeded at 15 sites, 10 of which had exceedances throughout the year. Pesticides had the greatest potential biological impact at the site with the greatest proportion of agricultural land use in its basin (the Maumee River, Toledo, OH, USA), with 72 parent compounds or transformation products being detected, 47 of which exceeded at least one benchmark value. Our risk-based screening approach identified multiple pesticide parent compounds of concern in tributaries of the Great Lakes; these compounds included: eight herbicides (metolachlor, acetochlor, 2,4-dichlorophenoxyacetic acid, diuron, atrazine, alachlor, triclopyr, and simazine), three fungicides (chlorothalonil, propiconazole, and carbendazim), and four insecticides (diazinon, fipronil, imidacloprid, and clothianidin). We present methods for reducing the volume and complexity of potential biological effects data that result from combining contaminant surveillance with HTS (in vitro) and traditional (in vivo) toxicity estimates. Environ Toxicol Chem 2022;00:1–18. Published 2022. This article is a U.S. Government work and is in the public domain in the USA. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.