Citizen science has the potential to support the delivery of the United Nations Sustainable Development Goals (SDGs) through its integration into national monitoring schemes. In this study, we explore the opportunities and biases of citizen science (CS) data when used either as a primary or secondary source for SDG 6.3.2 reporting. We use data from waterbodies that have both CS and regulatory monitoring in England and Zambia to explore their biases and complementarity. A comparative analysis of regulatory and CS data provided key information on appropriate sampling frequency, site selection and measurement parameters, necessary for more robust SDG reporting. The results show elevated agreement for pass/fail ratios and indicator scores for English waterbodies (80%) and demonstrate CS data can improve granularity and spatial coverage for SDG indicator scoring, even when extensive statutory monitoring programmes are present. In Zambia, management authorities are actively using citizen science projects to increase spatial and temporal coverage for SDG reporting. Our results indicate that design considerations for SDG focused citizen science can address local needs as well as provide a more representative indicator of the state of a nation’s freshwater ecosystems for international reporting requirements.