The California red-legged frog (CRLF), delta smelt (DS), and the California tiger salamander (CTS) are three species listed under the United States Federal Endangered Species Act (ESA), all of which inhabit aquatic ecosystems in California. The US Environmental Protection Agency (USEPA) has conducted deterministic screening-level risk assessments for these species potentially exposed to malathion, an organophosphorus insecticide and acaricide. Results from our screening-level analyses identified potential risk of direct effects to DS as well as indirect effects to all three species via reduction in prey. Accordingly, for those species and scenarios in which risk was identified at the screening-level, we conducted a refined probabilistic risk assessment for CRLF, DS, and CTS. The refined ERA was conducted using best available data and approaches, as recommended by the 2013 National Research Council (NRC) report Assessing Risks to Endangered and Threatened Species from Pesticides. Refined aquatic exposure models including the Pesticide Root Zone Model (PRZM), the Vegetative Filter Strip Modeling System (VFSMOD), the Variable Volume Water Model (VVWM), the Exposure Analysis Modeling System (EXAMS), and the Soil and Water Assessment Tool (SWAT) were used to generate estimated exposure concentrations (EECs) for malathion based on worst-case scenarios in California. Refined effects analyses involved developing concentration-response curves for fish and species sensitivity distributions (SSDs) for fish and aquatic invertebrates. Quantitative risk curves, field and mesocosm studies, surface water monitoring data, and incident reports were considered in a weight-of-evidence approach. Currently labeled uses of malathion are not expected to result in direct effects to CRLF, DS or CTS, or indirect effects due to effects on fish and invertebrate prey. This article is protected by copyright. All rights reserved.