Abstract Modern coastal environments are considered highly selective and dynamic, not only due to the natural variability of physical and chemical parameters, but also because of anthropogenic contamination. Our study aims to identify environmental and/or anthropogenic factors influencing benthic foraminiferal abundances over a period of one year in the Tramandaí-Armazém Lagoon, southern Brazil. Assemblages were composed exclusively of agglutinated species assigned to the genera Trochammina, Trochamminita, Ammotium, Haplophragmoides and Miliammina. Total abundances varied throughout the year, reaching the highest values during the wetter months of March and July, when living and dead assemblages became dominated by Ammotium salsum. This pattern is likely related to salinity fluctuations due to changes in freshwater input that, consequently, affected the amount of organic matter (e.g., phytodetritus) brought into the lagoon by surrounding drainages. To assess the impact of anthropogenic pollution, we evaluated total relative abundances of deformed tests in the Tramandaí-Armazém Lagoon. Relative abundances of deformed tests were the highest during the months of January and March, when contaminant (e.g., sewage) discharge was probably increased due to the seasonal population growth in the region.