We compared the sensitivity of algae and hermit crabs to seasonal shifts in the dominance of continuous sewage discharge vs. pulsed inputs of terrestrial material to a subtropical bay. During periods of low rainfall, when sewage was proportionately more important than diffuse loads from adjacent catchments, algae and crabs provided comparable information on the spatial distribution of N pollution. Conversely, during the wet season, when diffuse nitrogen loads from the catchment were of greater importance, the isotope signal of algae decoupled from that of crabs, indexing a greater magnitude of change and a more pronounced spatial gradient. Overall, algae better indexed the short-term impacts of anthropogenic nitrogen pollution whereas the signals provided by crabs provided a longer-term integrated measure of N inputs. Our results demonstrate the value of including multiple taxa with variable traits when monitoring the spatial and temporal extent of nitrogen inputs to coastal waters.