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Physicochemical parameters have been studied in the water column of Inkwell, Church, and Watling’s Blue Holes (San Salvador Island, Bahamas). Water samples were collected from multiple depths at the three blue holes to identify and characterize changes of physical and chemical parameters. The values were compared to the average ocean concentrations in order to assess how connectivity to the ocean, evaporation, freshwater input, and bacterial activity influence water rock interactions. The salinity concentrations vary between the surface and ~ -4 m in each blue hole before stabilizing to rather similar values (~19.6‰). Mixing processes in the water column at Inkwell and Church blue holes are inferred from changes in the concentration of chloride. The degree of variation is a mixed signal resulting from changes of the precipitation/evaporation balance and tidal driven water-rock interaction. Inkwell is strongly influenced by tidal pumping, which causes ample value fluctuations, most notably salinity (1.01 to 21.8‰), chloride (Cl-) from 300 to 9591.8 mg/L, and total hardness (9 to 293 mg/L) within the mixing zone. This location is the only site that may have a true halocline. Watlings’s geochemical parameters have the smallest range (i.e., salinity 30.19 - 34.30‰) due to a lack of mixing that suggests that this site has a direct conduit connection to the ocean. The furthest inland blue hole (Church) lacks significant geochemical fluctuations with the exception of Cl-, which changes from 19600 mg/L to 1800 mg/L between the depths of 1 and 2 m. The abrupt modification of Cl- values between surface and -2 m suggests mixing is occurring. The lack of other parameter variations within the water column suggests restricted flow via narrow conduits or more likely matrix flow. Salinity values decrease from the surface (21.47‰) to ~ -1 m (17.78‰) whereas, sulfate (SO42-) concentration at the same depth reach its maximum value (4009 mg/L). The high sulfate values throughout the column (2634 to 4009 mg/L) are characteristic of seawater (>2700 mg/L), thus indicating seawater seepage into the blue hole. We assume the elevated salinity values at the surface and -1 m are pointing towards evaporative processes.\u

Baseline physicochemical investigations on waters from three blue holes, San Salvador Island, Bahamas