A detailed mass balance that evaluates nutrient inputs and outputs is fundamental to determining the most promising strategies to mitigate eutrophication and its undesirable effects. However, such analyses are rare in Brazilian urban ponds where water quality impairment remains a significant issue. We performed a mass balance to identify the main phosphorus (P) sources in a hypereutrophic tropical shallow urban pond. We used the PCLake model to estimate the P loading required to reduce phytoplankton biomass. The water column was considered the primary unit in the model. The P balance was calculated from external inputs, internal inputs from bed sediment to the water column, and outputs from the water column through surface water outflow and to the bed sediments over a full hydrological year. The total P input into the pond water (external and internal) was 35.3 mg m−2 d−1 and the output was 35.2 mg m−2 d−1. The P balance revealed that contributions to the water column from external and internal sources were 82.5% and 17.5%, respectively. Birds were the main contributor to P input (76.0%). The highest P loss from the water column was to the sediment (97.6%). Most of the P leaving the water column to the sediment was retained in the sediment, and part was returned to the water column through internal loading. Measures to reduce eutrophication in this pond should focus on integrated management to decrease both the external and internal P sources by managing birds and avoiding P release from sediment, and to decrease water residence time in the pond.