This study investigated the effects of potentially toxic elements (PTEs) on the spatial distribution of benthic foraminifera in Jobos Bay, a National Estuarine Research Reserve in Puerto Rico. High PTE total concentrations (Cr-Cu-Zn-Mn-Hg) clustered around anthropogenic sources where “moderately polluted” to “moderate-heavily polluted” conditions prevail. The spatial distribution of the foraminiferal ecological indices mainly followed trends in bioavailable (exchangeable and organic-bound) PTEs. Ammonia (T1) (36%) was the most abundant foraminifera with species richness and diversity being characteristically low for an impacted estuary in Puerto Rico. Based on the Foram Stress Index, the ecological quality status (EcoQ) of the benthic environment varied according to PTE pollution and water quality levels with a “heavy polluted” (EcoQ “poor”) Inner Bay area (east coast) proximal to multiple non-point sources of pollution while conditions improved towards “moderately polluted” (EcoQ “moderate”) in the Open Bay area. The Restricted area (west coast of the bay) which received direct effluents of raw sewage was exposed to higher organic-bound bioavailable PTE concentrations coupled with more corrosive and less oxygenated bottom waters in some areas. This variability was reflected in the “heavy polluted” (EcoQ “poor”) and “azoic” (EcoQ “bad”) conditions where several sites were barren with respect to porcelaneous taxa in addition to Ammonia (T1) being almost absent in one sample.