Increasing atmospheric carbon dioxide and its dissolution in seawater have reduced ocean pH and carbonate ion concentration with potential implications to calcifying organisms. To assess the response of Caribbean benthic foraminifera to low carbonate saturation conditions, we analyzed benthic foraminifera abundance and relative distribution in proximity to low carbonate saturation submarine springs and at adjacent control sites. Our results show that the total abundance of benthic foraminifera is significantly lower at the low pH low calcite saturation submarine springs than at control sites, despite higher concentrations of inorganic carbon at the spring sites. The relative abundance of symbiont-bearing foraminifera and agglutinated foraminifera was higher at the low pH low calcite saturation submarine springs compared to control sites. These differences indicate that non-symbiont bearing heterotrophic calcareous foraminifera are more sensitive to the effects of ocean acidification than non-calcifying and symbiont bearing foraminifera, suggesting that future ocean acidification may impact natural benthic foraminifera populations.