Effect-based monitoring using in vitro bioassays and well plate-based in vivo assays has been recommended for water quality monitoring as they can capture the mixture effects of groups of chemicals that elicit the same mode of action. Applied as a complementary tool to targeted chemical analysis, effect-based monitoring can provide valuable input for risk analysis and risk management through Water Safety Plans (WSP). This report aims to help support the integration of effect-based monitoring into WSP frameworks by providing protocols and developing decision-making tools to assist both laboratory staff and WSP teams.