Here we provide data from water samples that were collected twice monthly, from April 26, 2021 and April 25, 2024, from sixteen stations throughout the San Juan Bay Estuary, Puerto Rico. The station locations are given in Fig. 1 and the descriptions of the data headers in the dataset are given in Table 1 in the associated Read Me file. An overview of methods follows. For methodological details, please see Oczkowski et al. 2026, Water column biogeochemistry in a tropical estuary. This dataset is associated with the following publication: Oczkowski, A., I. Cappielo-Cosme, M. Schwartz, N. Soto Nieves, M. Molina, E. Villafane, E. Huertas, D. Katz, and A. Hanson. Water column biogeochemistry in a tropical urban estuary. JOURNAL OF TROPICAL ECOLOGY. Cambridge University Press, Cambridge, UK, 42: e2, (2026).