We examined the recovery of a fish assemblage following the catastrophic spill of highly alkaline (pH ~13) red sludge into a lowland river (i) to characterize taxonomic- and trait-based colonization of fishes in the river in the first 3 years of the recovery and (ii) to determine which structural- and trait-based variables best predicted colonization. Species richness showed comparable values to pre-disturbance state <1 year after the spill. We found only moderate changes in the dominance of the most abundant species between pre- and post-disturbance periods, and consistent changes in the relative abundance of some rare species during the post-disturbance period. Frequency of occurrence (%) of the fishes in the watershed and their relative abundance (%) proved to be the most important predictor variables in colonization, whereas trait-based variables had a less important role. Our study about one of the largest scale and most serious documented fish kill shows that both taxonomic- and trait-based structure of fish assemblages can regenerate remarkably fast in a modified river and also shows that unfortunate chemical spills provide insights into the assembly of stream fish assemblages.