Coral reefs are currently exposed to a number of anthropogenic pressures worldwide. With ocean warming and acidification expected to continue in the near future, it is important to study coral environments within natural oceanographic gradients, particularly with respect to their effects on environmental indicator species. Benthic foraminifera are sensitive to environmental change, making them ideal indicators of reef water quality and health. Hence, we studied benthic foraminifera from samples collected throughout the Galápagos Archipelago, an equatorial island chain strongly influenced by the El Niño–Southern Oscillation (ENSO) and deep water upwelling—resulting in an atypical natural temperature, nutrient, and pH transition zone throughout the tropical latitudes of the archipelago. While foraminiferal abundances averaged 0.7% of all sand-sized carbonate grains, assemblages were characterized by a total of 161 species in 72 genera. The northern archipelago was dominated by Miliolida and contained the highest percentages of symbiont-bearing taxa in the Galápagos. However, the archipelago as a whole strongly favored heterotrophic Rotaliida, particularly throughout the southern islands, which are directly impacted by high nutrient and low pH upwelling from the Equatorial Undercurrent (EUC). While the Eastern Tropical Pacific does not show the diversity of its western counterpart, Galápagos foraminiferal assemblages revealed a relatively high foraminiferal diversity for the region as well as evidence in support of earlier reports of high endemism within the archipelago.