A recent analysis of fish assemblages in the Goulburn River, south-eastern Australia, used fish survey data collected between 1970 and 2002 to examine spatial patterns in the compositions and relative abundances of fish assemblages in the catchment. Based on this analysis, it was concluded that the native fish fauna of the Goulburn River is in a stressed condition and that introduced species dominate the fish assemblages. Fish survey data collected in 1982–1983 are compared with data collected in 2003–2004 to examine whether fish assemblages in the lower Goulburn River were stable at the temporal scale at which the data were aggregated in the previous analysis. The results show significant differences in fish assemblage composition between the two surveys, suggesting that fish assemblage structure in the lower Goulburn River did not remain stable between 1982–1983 and 2003–2004. The aggregation of data collected over several decades has the potential to confound analysis of spatial variations in fish assemblages and is unlikely to provide a reliable means of assessing their current condition.