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The complexity of estuaries allows for the establishment of diverse communities composed of species with different survival strategies. The vertical migration of animals in the sediment is linked to competition, escape from predators and adaptations to diurnal physio-chemical changes related to variations in water levels. The present study aimed to evaluate niche overlap and amplitude, as well as the composition and structure, of communities of polychaetes and molluscs between sediment aliquots during the day and at night. Data sampling was performed in the Tubarão River estuary. The highest individual occurrence was registered during the diurnal period. Communities of polychaetes varied significantly between sediment aliquots during the day and at night, while molluscs did not show diurnal variation. Niche overlap results for polychaetes showed higher values between aliquots during the night, while molluscs showed greater overlap during the day. This indicates that polychaetes and molluscs have different mechanisms of coexistence. This may be related to different attributes of species allowing for the division of resources among individuals. Examination of niche overlap provides insights into coexistence of mechanisms within benthic macroinvertebrate communities. [ABSTRACT FROM AUTHOR]