Point and nonpoint sources of phosphorus (P) and nitrogen (N) can cause reductions in water quality, including eutrophication. Nonpoint pollution represents a special challenge because of dispersed not easily identifiable sources such as the runoff from soil, nutrients, and other chemicals from agricultural fields and residential areas. Laguna Cartagena is a tropical freshwater wetland, situated in southwestern Puerto Rico. It is a eutrophic ecosystem, and its eutrophication is caused by both external nutrient loading and internal, mainly by phosphorus. This wetland has been affected by phosphorus loading from inorganic agricultural fertilizer in this historically oligotrophic wetland system until the end of subsidized fertilizer use and sugar cane cultivation in the late 1990s. This study identifies: 1) nonpoint sources of phosphorus (SRP, Soluble Reactive Phosphorus and TP, Total Phosphorus) and nitrogen (nitrate, nitrite, and ammonia) that enter Laguna Cartagena; and 2) the role of precipitation events on the contributions of phosphorus and nitrogen loading to ecosystems. Herein we assess water samples from five channelized external sources of P and N that enter Laguna Cartagena at two-week intervals from October 2013 through November 2014. Rainfall data were obtained weekly from a rain gauge. Standard methods were used for all chemical analyses. Results showed that the channelized waterways that carry water to the lagoon can be classified as hypereutrophic (>100 μg/L) for TP concentrations and oligotrophic (<200 μg/L) for nitrogen concentrations. Currently agriculture (rice and cattle) is the predominant land use at the nearby University of Puerto Rico (UPR) Lajas Agricultural Experiment Substation, the predominant nonpoint source of nutrient pollution (SRP, TP and ammonia) in the principal channelized water sources to the lagoon. Current nutrient loads are likely derived from fertilizers applied to the Substation’s rice fields, and a high density livestock. The second important cause of external surface water degradation (SRP, TP and ammonia) is the discharge from rural households in the drainage basin that discharge greywater directly to the environment, as indicated by the results from Cerro Alto hills immediately to the north of the lagoon. Precipitation also was associated with SRP, TP and ammonia loads.