Foraminifers are important lower trophic-level members of oceans and estuaries, and study of their populations provides information about the health of an ecosystem. Replicate cores were taken at five stations in Nueces Bay, Texas, to evaluate living foraminifers in this heavily impacted estuary. A shallow secondary bay, Nueces Bay is naturally stressed and receives point-source and non-point-source effluents from the Nueces River and various industries. Most of the industries are clustered on the south shore of the bay, which also has a power plant and a shipping channel. The north shore, in contrast, is nearly devoid of industry and habitation. Since salinities in the bay vary due to freshwater influence, foraminiferal populations were sampled mid-bay, and spaced on a north-south transect where conditions are most constant. Results show that living densities and species richness are much higher at the south shore, probably due to the proximity of river inflow. In addition, foraminiferal communities are different at the northern and southern shores, as shown by statistical analyses. A high percentage of living foraminifers, almost exclusively Ammonia, have damaged shells, with a few chambers to entire whorls missing. This shell loss is attributed to dissolution. Framboidal pyrite found in living tests in oxygenated sediments is a stress response to heavy metal contamination, and pyritization may contribute to acidic conditions responsible for dissolution. Such dissolution is usually associated with diagenesis, but apparently can occur extensively in living individuals. The study cautions against assuming that lower densities, species richness, and shell dissolution along a transect are due solely to anthropogenic rather than natural causes.