The initial effects of the toxic waste spill in April 1998 at the Aznalcóllar mine (SW Spain) on the nektonic community of the Guadalquivir Estuary were examined at three sampling sites using univariate and multivariate techniques. Since studied communities showed a considerable seasonal trend, only seasonally homogenous periods were compared to analyse effects of the spill: May-August 1997 (before spill) and May-August 1998 (after spill). Results of both techniques (two-way nested ANOVA and ANOSIM tests, P > 0.05) indicated that there was no significant difference between the nektonic community of the estuary before and after the spill (monthly number of species, abundance, biomass and similarity among samples). Conversely, an unusually high density was observed at the outer sampling site immediately after the spill for species typical of more stagnant estuarine habitats. This feature seems to indicate that the fauna in the estuarine area through which the untreated water penetrated into the main course may have been disturbed. Results also suggest that this initial sudden input of fresh water to the estuary could have enhanced the effects of an increased river flow (a drop in the salinity). Nevertheless, longer temporal series of data, especially for permanent estuarine inhabitants, are recommended before conclusions can be drawn on the effects of the toxic waste spill on estuarine communities.