| Summary: | Abstract This study was conducted in the Itajaí-Açu river lower estuary in Southern Brazil, in which we aimed to: (1) analyze spatiotemporal variations on the macrofauna; (2) search for relationships between environmental variables and the assembly and (3) evaluate the influence of capital dredging upon the assembly. Two hundred twenty eight samples were performed in four stations, two of which affected by dredging. Sediment (sand, silt and clay, organic matter and carbonate) and water column´s variables (temperature, salinity, pH, dissolved oxygen, and turbidity) were also assessed. We applied Principal Component Analysis for environmental variables and Hierarchical Clustering for biotic data. Correlations between environmental and biotic matrices were tested by Canonical Analysis of Principal Coordinates. Spatiotemporal variations in the assembly were tested by Permutational Multivariate Analysis of Variance. From the 21.839 organisms sampled, 97% was represented by the gastropod Heleobia australis. Despite the influence of the river discharge on the ecosystem, dredging was deleterious to the assembly, favoring opportunistic organisms such as H. australis.
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