The present study highlights the difficulty of linking a single environmental variable or set of conditions to the ecology of a waterway, particularly over a short period, as the LQI results suggest. Biotic scores did not clearly reflect trends in environmental variables but these also varied between sites. The multivariate analysis of highly contrasted years gave a much clearer picture of the influence of environmental variables on biotic communities. Flow rate was highly important during drought years, and this determined how greatly other environmental variables influenced communities.