Coastal zones throughout the world are subject to natural and anthropogenic disturbances that modify the natural assemblages. The present study determined the response of the assemblage of macrobenthic invertebrates to the presence of a pier and natural climatic variations. Two analytical models were considered; one was an asymmetric model that permitted the comparison of the sector closest to the pier (impact) with the average of the sectors located further away (controls); the other was a three-way model that enabled the three sectors within the area to be analysed. With both models, the differences were compared among the sampling periods and the scale at which the variation in the data was greatest. No differences were detected among individual sectors or between the control and impact sectors. However, significant differences were found among the four periods. The zone closest to the pier presented greater temporal variability. This relationship suggests that the pier affecting the assemblage and the impact may be increased by the climatic conditions prevalent in the zone. It is necessary to establish a broader temporal analysis and a more detailed analysis of the structure and composition of the benthic assemblage to elucidate this temporal and spatial variability.