Biogeochemical hotspots can be driven by aggregations of animals, via excretion, that provide a concentrated source of limiting nutrients for primary producers. In a subtropical seagrass ecosystem, we characterized thresholds of ecological change associated with such hotspots surrounding artificial reef habitats. We deployed reefs of three sizes to aggregate fishes at different densities (and thus different levels of nutrient supply via excretion) and examined seagrass characteristics that reflect ecosystem processes. Responses varied as a function of reef size, with higher fish densities (on larger reefs) associated with more distinct ecological thresholds. For example, adjacent to larger reefs, the percentage of P content (%P) of seagrass (Thalassia testudinum) blades was significantly higher than background concentrations; fish densities on smaller reefs were insufficient to support sharp transitions in %P. Blade height was the only variable characterized by thresholds adjacent to smaller reefs, but lower fish densities (and hence, nutrient input) on smaller reefs were not sufficient for luxury nutrient storage by seagrass. Identifying such complexities in ecological thresholds is crucial for characterizing the extent to which biogeochemical hotspots may influence ecosystem function at a landscape scale.