Benthic foraminifera were collected from reef coral, seagrass and mangrove sediments of Almirante Bay, Caribbean Panama, to associate species and assemblages with habitats and environmental conditions related to degraded water quality. The three habitats occur in different adjacent areas within an embayed, patch-reef setting. We analyzed the relative abundance, diversity and community structure of benthic foraminiferal species > 63 µm in 17 sediment samples from < 2 m mean water depth. Results from hierarchical cluster analysis, analysis of similarity, similarity percentages, non-metric multidimensional scaling and Fisher's alpha diversity were compared from seagrass, mangrove and coral habitats and also between two areas with contrasting water quality as previously defined by hydrography and general water quality.

Among the three neighboring habitats, assemblages are fairly similar but differ in species proportions. Overall, Ammonia parkinsoniana, indicative of relatively low and variable salinities, is a dominant taxon. Foraminiferal assemblages from mangroves had the lowest mean diversity, a common trend under reduced salinity conditions, and diversity appears to be regionally controlled by freshwater input. Planorbulina acervalis was dominant in seagrass beds. Low-diversity, stress-tolerant foraminiferal assemblages are present in samples from all three habitats, reflecting the bay's highly variable patch-reef structure, freshwater input, and possible hypoxia. Diversity is generally lower near the mainland than in the eastern bay off the island of Isla Colón. Environmental associations of the benthic foraminifera of Almirante Bay are baseline ecologic data for comparisons to coastal habitats formed before human occupation and have the potential to be used in the sedimentary record to assess the impact of anthropogenic disturbance.

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