The macrofauna community structure at two distinct environments (i.e., a pond and a sedimentation basin) of a shrimp farm was compared to the natural environment across entire cycle of Litopenaeus vannamei culture located at estuarine region of the Patos Lagoon, southern Brazil. Both farm habitats showed lower values of number of species and density (pond: 1spp. and 8 ind./0.008m2; sedimentary basin: 3spp. and 12 ind./0.008m2) compared to natural environment (6spp. and 40 ind./0.008m2). However, the biomass values at sedimentary basin (mean = 0.06 g/0.008m2) were twice higher than natural environment. At pond, low richness of macrofauna seems related to absence of previous pond preparation; while shrimp predation and/or disturbance resulting in low densities after begin of culture. Otherwise, the presence of a biota relatively abundant and with high biomass at sedimentary basin could contribute to increase effluent quality of the shrimp farm.