Coastal lagoons are common features of the Puerto Rico shoreline that provide habitat for commercial and recreational species and serve important roles in the nutrient cycle of the ecosystems. The U.S. Geological Survey, in cooperation with the Puerto Rico Environmental Quality Board, conducted a limnological study at Caño Boquerón in Cabo Rojo and at Puerto Mosquito on Isla de Vieques, Puerto Rico, to assess the principal mechanisms affecting the hydrology and water-quality characteristics of these coastal lagoons and provide baseline information to the regulatory agencies responsible for the management and conservation of these coastal waters and the preservation of their aquatic life.

Field measurements and water samples were collected and processed during July 2015–July 2016 for analysis of physical, chemical, biological, and bacteriological characteristics. In addition, bathymetric surveys were made and sediment cores were collected in each lagoon to determine water volume and sediment deposition rate. Physicochemical properties assessed at Caño Boquerón indicated values were generally in compliance with Puerto Rico Environmental Quality Board standards; turbidity was occasionally slightly greater than the established standards, and dissolved oxygen concentration at bottom depths was lower than standards limits. Water transparency was evaluated through the Secchi disk method, and the average depth of disappearance was 1.0 meter (m) for Caño Boquerón and 1.9 m for Puerto Mosquito.

Assessment of biological characteristics at both sites included primary productivity calculations as well as carbon production equivalents and monthly water sampling for bacteriological and nutrient analyses. For Caño Boquerón, gross plankton primary productivity averaged 3.38 grams of oxygen per cubic meter per day (gO₂/m³-d); this value was computed as the sum of net phytoplankton primary productivity (0.74 gO₂/m³-d) and plankton respiration (2.64 gO₂/m³-d). Net community primary productivity averaged 1.44 gO₂/m³-d, and the community respiration rate averaged 8.10 gO₂/m³-d, which indicates that the biological community, aside from phytoplankton, acts as a net consumer rather than a net producer of biomass. In Puerto Mosquito, gross plankton primary productivity averaged 2.07 gO₂/m³-d, of which 0.39 gO₂/m³-d could be ascribed to net phytoplankton primary productivity, and 1.68 gO₂/m³-d could be ascribed to plankton respiration. Diel studies conducted at Puerto Mosquito reflected an average net community primary productivity of 2.43 gO₂/m³-d, and the average respiration rate was 6.72 gO₂/m³-d.

In a bathymetric survey conducted in August 2015, the water volume for the Caño Boquerón lagoon was calculated as 967,000 cubic meters (m³), and the water volume at Puerto Mosquito was calculated as 1,182,200 m³, with an average depth of 1.5 m for Caño Boquerón and 1.8 m for Puerto Mosquito. The daily seawater exchange for Caño Boquerón and Puerto Mosquito was 13 and 5 percent of their water volumes referenced to mean sea level, respectively. A total of 20 sediment samples were processed and analyzed for cesium-137 (¹³⁷Cs) and lead-210 (²¹⁰Pb) radioisotopes. Analyses indicated that the sediment deposition rate at Caño Boquerón ranged from 0.32 to 0.36 centimeter per year, based on age dating analysis of ¹³⁷Cs and ²¹⁰Pb data; in Puerto Mosquito, the sediment deposition rate ranged from 0.26 to 0.27 centimeter per year, based on ¹³⁷Cs and ²¹⁰Pb data.

Bacteriological analyses at Caño Boquerón and Puerto Mosquito indicated that fecal coliform and enterococci concentrations were below Puerto Rico Environmental Quality Board standards during the study. The highest concentrations of fecal coliform (22 colonies per 100 milliliters) and enterococci (9 colonies per 100 milliliters) at Caño Boquerón occurred in July, which coincided with the busiest season of vacation rentals near the lagoon. Bacteria concentrations were generally lower in Puerto Mosquito than in Caño Boquerón; maximum concentrations of fecal coliform and enterococci bacteria were measured in November 2015. The potential sources of contamination for Puerto Mosquito are limited, because it is within a conservation area.