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The US Environmental Protection Agency must evaluate potential impacts on federally listed threatened and endangered species during pesticide registration. However, current deterministic methods for analyzing geospatial co-occurrence between listed species locations and pesticide use sites fail to account for spatial and temporal uncertainty in both species occurrence and pesticide use. To address this challenge, we developed the Automated Probabilistic Co-Occurrence Assessment Tool (APCOAT). Through multiple case studies, we demonstrate how incorporating probability and uncertainty can improve both species conservation planning and regulatory decision-making.