Large quantities of anthropogenic nitrogen (N) in the marine environment are detrimental for coastal ecosystems and understanding the magnitude and distribution of this N opens paths to remediation. One area of concern is Cocos Lagoon, in the south of Guam, Northern Mariana Islands, which hosts a diversity of corals including Acropora species listed in the Endangered Species Act. Degradation of Guam's coral reefs may be influenced by untreated sewage effluent. To gain insight into the spatial extent of human N pollution, we deployed 50 macroalgal thalli (Padina sp.) as bio-indicators in a grid pattern over the entire lagoon for one week and then measured the stable N isotopes of bio-available N (δ¹⁵N). We observed relatively low δ¹⁵N values (∼1–2‰) in the shallow areas in the east suggesting coastal currents bringing in fixed N from the open ocean or local N₂ fixation. The comparatively high δ¹⁵N values (∼6‰) in the deeper channel of the lagoon suggest sewage as a major source of N. The distribution of δ¹⁵N values was not determined by the distance to N sources, such as river outlets or the tourist resort on Cocos Island but by the bathymetry, which affects the residence time and influx of oceanic water.