The Springs Coast of Florida, USA (northeast Gulf of Mexico), includes an extensive system of springs and spring-fed streams that discharge billions of liters of water daily. The spring waters have high alkalinity and high calcium concentrations due to the Paleogene limestone lithology of this region. Benthic foraminifers are abundant on the shallow shelf, including Archaias angulatus which hosts chlorophyte symbionts. This study was motivated by the hypothesis that areas of discharge from limestone lithofacies may provide refugia for calcifying organisms during ocean acidification. Environmental data and sediment samples were available from 41 sites at depths <8 m. Benthic foraminiferal species identified (142) included 65 porcelaneous, 65 hyaline, and 12 agglutinated taxa, with 13 species sufficiently common to make up ≥2% total relative abundance. Overall, 58% of the specimens were porcelaneous and most of the remainder were hyaline. Smaller miliolids dominated in samples from most of the inshore polyhaline sites (22–30), while hyaline taxa co-dominated the more offshore sites (salinities >30), representing a distribution reversal compared to previous reports from Gulf of Mexico coastal habitats. The elevated alkalinity and calcium ion concentrations associated with freshwater discharge from limestone lithofacies allows Ar. angulatus and small miliolids to thrive in polyhaline waters.