Some coral reefs, such as patch reefs along the Florida Keys reef tract, are not showing significant reductions in calcification rates in response to ocean acidification. It has been hypothesized that this recalcitrance is due to local buffering effects from biogeochemical processes driven by seagrasses. We investigated the influence that pore water nutrients, dissolved inorganic carbon (DIC) and total alkalinity (TA) have on aragonite saturation states (Ωaragonite) in the sediments and waters overlying the sediment surfaces of sand halos and seagrass beds that encircle Alinas and Anniversary reefs in Biscayne National Park. Throughout the sampling period, sediment pore waters from both bottom types had lower oxidation/reduction potentials (ORP), with lower pH relative to the sediment surface waters. The majority (86.5%) of flux rates (n = 96) for ΣNOx–, PO43–, NH4+, SiO2, DIC and TA were positive, sometimes contributing significant concentrations of the respective constituents to the sediment surface waters. The Ωaragonite values in the pore waters (range: 0.18 to 4.78) were always lower than those in the overlying waters (2.40 to 4.46), and 52% (n = 48) of the values were <2.0. The DIC and TA fluxes at the sediment–water interface reduced Ωaragonite in 75% (n = 16) of the samples, but increased it in the remainder. The elevated fluxes of nutrients, DIC and TA into the sediment–water interface layer negatively alters the suitability of this zone for the settlement and development of calcifying larvae, while enhancing the establishment of algal communities.