These data are from the article “Seasonal carbonate chemistry dynamics on southeast Florida coral reefs: localized acidification hotspots from navigational inlets” published in Frontiers in Marine Science. The data in this package were collected from inlets and reefs along the coast of Southeast Florida. Water was collected bi-monthly from four reefs (Oakland Ridge, Barracuda, Pillars, and Emerald) and three closely-associated inlets (Port Everglades, Bakers Haulover, and Port of Miami). Water samples were collected at these locations either at the surface (~1m depth) or immediately above the benthos measured using a rosette sampler (ECO 55, Seabird). Temperature was recorded at each depth using a CTD (SBE 19V2, Seabird). Turbidity (NTU) was measured at time of water collection. Once collected, water samples were transferred to borosilicate glass bottles, samples were fixed using 200 µL of HgCl2 and sealed using Apiezon grease and a glass stopper. Salinity was measured using a densitometer (DMA 5000M, Anton Paar), while total alkalinity (TA) and dissolved inorganic carbon (DIC) were determined using Apollo SciTech instruments (AS-ALK2 and AS-C3, respectively). All values were measured in duplicate and corrected using certified reference materials following recommendations in Dickson et al. (2007). Aragonite saturation state (ΩArag.), Calcite saturation state (ΩCa), pH (Total scale), and the partial pressure of CO2 (pCO2) were calculated with CO2SYS (Lewis and Wallace, 1998) using the dissociation constants of Mehrbach et al. (1973) as refit by Dickson and Millero (1987) and Dickson (1990). Water samples were reserved for nutrient analyzed at time of collection to determine Total Kjeldahl Nitrogen, Total Phosphorus, and fluorescence of Chlorophyll-a. This research was supported through NOAA’s Coral Reef Conservation Program.