The understanding of the differences between living (L) and dead (D) benthic foraminiferal assemblages and all the factors that might lead their distribution should be a key to characterize the environmental and paleoenvironmental changes accurately. Population dynamics and dissimilarities of biological nature (the differences in turnover rate and seasonal alterations in standing stock) can cause significant divergences between the L and D foraminiferal assemblages. This study compares L and D foraminifera to evaluate the sediment quality of the Brazilian Saquarema Lagoon System (SLS) using biogeochemical proxies and predict how coastal ecosystems are responding to the combined effects of eutrophication and pollution pressure and areas where the paleoenvironmental studies can be performed. The SLS is a transitional environment where total organic carbon, proteins, and dissolved oxygen are the main factors controlling the distribution of foraminiferal assemblage. The high values of biopolymers (carbohydrates, lipids, and proteins) in SLS indicate a very impacted environment with long water residence time. The low values of species richness, Shannon-Weaver diversity, and evenness for both L and D foraminiferal assemblages are a consequence of fluctuating conditions in the SLS. Due to low salinities, agglutinated species and Quinqueloculina seminula can occur in the most confined areas, and Ammonia parkinsoniana, Cribroelphidium excavatum, Cribroelphidium poeyanum, and Elphidium gunteri characterized the area with the highest marine influence. Although in most of the SLS the taphonomic processes modified the original assemblage, in some regions the thanatocoenosis corresponds to the biocenosis. These areas can be considered the most suitable for future paleoenvironmental and paleoclimatic studies.