Mangroves provide numerous ecosystem services, including biodiversity values such as nesting sites for piscivorous waterbirds. High concentrations of waterbirds at nest sites are hypothesized to affect ecosystem dynamics, yet few studies have examined their effects as a nutrient source in mangroves. We examined the effects of nutrient enrichment by colonial waterbirds at a mangrove rookery in the Gulf of Fonseca, Honduras. We compared nutrient inputs via bird guano deposition and macronutrient levels in the vegetation and soils between a small island that hosted large numbers of roosting waterbirds and an adjacent island with little evidence of waterbird activity. Nest density at the rookery was 1721 ± 469 nests ha-1. Rookery birds deposited 7.2 ± 3.4 g m-2 day-1 guano dry weight, delivering an estimated 1.12 Mg ha-1 nitrogen and 0.16 Mg ha-1 phosphorus to the island over a 120 day breeding season. This large nutrient influx contributed to substantially higher concentrations of biologically important nutrients in the rookery soils (seven times more plant available phosphorus, eight times more nitrate, and two times more ammonium). Rookery mangrove leaves contained significantly higher concentrations of nitrogen and phosphorus compared to the control site. These results suggest that colonial waterbirds significantly influence nutrient dynamics of mangroves at local scales. Further research is needed to understand the effects of avian derived nutrients on mangrove growth rates, nutrient export to adjacent waters, invertebrate communities, and mangrove associated fisheries.