Pohnpei, Federated States of Micronesia, is a coral reef biodiversity hotspot. However, little water quality data are available, especially for nearshore waters. Identifying land-based pollution sources for watershed management is a priority of the government to improve water quality for their people and reefs, and it is needed before further development and climate change exacerbate conditions. We conducted an island-wide nearshore water quality survey in 2018 and 2019 to establish current conditions through nutrients, fecal indicator bacteria, stable nitrogen isotopes in nitrate and macroalgal tissue measurements. Relationships among water quality parameters and land cover were examined to identify drivers of water pollution. Sewage pollution from wastewater treatment plant infrastructure and onsite sewage disposal systems, piggeries, and dredge sites all contributed to poor water quality largely in the municipalities of Kolonia and Sokehs. NO3- + NO2-, Enterococcus spp., and δ15N-NO3- were the best indicators of sewage pollution, and the former two were positively related to urban cover. δ15N in macroalgae tissue was not a good indicator of sewage pollution because of high coastal NH4+ concentrations from mangroves. Our results will inform management actions to improve water quality, but more explicit measurements relative to pollution sources, transport mechanisms, and watershed information are needed. Our study's approach will be useful for other locations in the region grappling with nearshore water quality issues.