ABSTRACT: The excessive nutrients discharge from industrial and domestic sources have been contributing to the establishment of eutrophication conditions, particularly in chocked lagoons in the Neotropical region. This study evaluates the influence of organic matter on the foraminiferal and ostracode assemblages by combining biopolymers concentrations, sediment grain size, and physical and chemical parameters in the Marica-Guarapina Lagoon System (MGLS, Rio de Janeiro, Brazil). The physical-chemical parameters show a well-defined confinement gradient from the channel to the innermost region. The biopolymers analysis indicates that the Guarapina and Barra Lagoons are characterized by the highest values of organicmatter from anthropic origin. Living organisms are absent or poorly represented in most of these regions of Marica and Barra lagoons. Seventeen living species of foraminifera and five of ostracodea are identified in the MGLS. Foraminifera and ostracodea exhibit a negative relationship with organic matter as evidenced by statistical analysis. Quinqueloculina seminula (foraminifera) and Cyprideis spp. (ostracodea) are associated with shallow and sandy regions and Ammonia spp. to eutrophic areas. The cluster analysis identifies six distinct regions in theMGLS based on species distribution and their relationship with environmental parameters: I - a region under the influence of marine waters; II - shallow and sandy region with high concentrations of proteins; III - a region characterized by high aerobic microorganisms activity; IV - an impacted region that is the channel passage between the lagoons; V - the most stressed region of the lagoons; and VI - the most confined area of the MGLS.