The dataset contains the selected physical properties and chemical constituents that were measured at Caño Boquerón, Cabo Rojo, and Puerto Mosquito, Isla de Vieques, Puerto Rico during a diurnal cycle. Two diel studies were conducted per lagoon to determine the community primary productivity. Photosynthesis creates oxygen which enhances microbiological activity and results in the production of organic matter. Primary productivity is important for supporting the food web in aquatic ecosystems. The field data collection included the measurement of temperature, dissolved oxygen, and percent of oxygen saturation. Measurements were obtained at about 1 hour intervals. Diel studies were conducted on October 29, 2015 and March 2, 2016 at Caño Boquerón, Cabo Rojo, Puerto Rico, and on November 17, 2015 and March 9, 2016 at Puerto Mosquito, Isla de Vieques, Puerto Rico.