Urbanised coastlines are affected by cumulative impacts from a variety of anthropogenic stressors, but spatial information on the distribution of these stressors at the local scale is scarce, hindering the ability of managers to prioritise mitigation options. This work investigated the spatial footprint of land-based nitrogen discharges to a metropolitan coastline and assessed the potential role of this stressor alone on seagrass dynamics at the scale of the ecosystem. The macroalga Caulocystis cephalornithos was used as a time-integrative sampler of nitrogen in the water column over 202 sites monitored across an area of ~800 km2. The stable isotopic signature of nitrogen in tissues (δ15N) was used to map plumes of anthropogenic origin. The surface area of these plumes was found to be proportional to nitrogen loads from land. The largest plume was associated with discharges from an industrialised estuary and a wastewater treatment plant, where a monthly nitrogen load in excess of 110 tonnes affected an area >80 km2. The location and size of the plumes changed with seasons as a result of wind forcing and rainfall/wastewater reuse. The location of the plumes was compared to published seagrass distribution obtained from video transects. Dense seagrass meadows only occurred in areas unimpacted by plumes throughout the year, mostly in shallow (<5 m) regions for Amphibolis antarctica, and deeper (5-10 m) for Posidonia sp., possibly as a result of this species higher tolerance of low light conditions. This higher tolerance might also explain why Posidonia sp. is observed to preferentially recolonise areas of previous loss in the region. While a decrease in the spatial footprint of nutrient plumes has created conditions for natural seagrass recolonisation in some areas, it did not halt seagrass loss in others, suggesting the influence of additional stressors such as wave dynamics and light attenuation due to turbid/coloured stormwater.