Many researchers report abnormal test morphologies in benthic foraminifers and some suggest that anthropogenic pollution may be one of the causes for these anomalies. Some species are even used as bioindicators of anthropogenic pollution. However, environmental stress may be exerted by natural factors also, such as hypersalinity, periodical acidification and strong hydrodynamics. We observed large populations of morphologically abnormal foraminifer individuals in 227 recent sediment samples on the southwestern coast of Antalya (Turkey). In 117 of our samples we found morphologically abnormal Textularia bocki Höglund individuals. The proportion of abnormal individuals to normal ones within a population is 3.2%. We also found morphologically abnormal individuals of Peneroplis arietinus Batsch, P. pertusus (Forskål), P. planatus (Fichtel and Moll), Amphisorus hemprichii Ehrenberg, Sorites orbiculus Ehrenberg, S. variabilis Lacroix and Spiroloculina cf. S. angulata d'Orbigny in 87 of our sediment samples. The abundance and large sizes of these abnormal individuals are significant. There is no industrial plant near the study area and this region is not a popular tourist attraction. Thus, anthropogenic waste cannot be regarded as an important cause for unhealthy foraminifers in this region. There are frequent freshwater springs along the coast around Kalkan, Kaş and eastern Kekova. Seasonal discharge from submarine caves also contributes freshwater to the sea ranging between 12% and 50%. Radioactivity levels and heavy metal concentrations in these submarine discharges are insignificant. However, we see a correlation between the abundance of abnormal individuals and the locations of caves and freshwater springs in the region. Our results suggest that rapid changes in ecological parameters related to submarine groundwater discharge may be responsible for morphological anomalies in foraminiferal genera and species.