River damming and associated reservoir causes intense and dramatic changes that create new environments, with particular structure and functioning. In these systems, flow control and artificial variations in water level are important determinants of the structure of fish assemblages. Planned reduction in water level (drawdown) is used to manage productivity in reservoirs. However, the effects of non‐planned reductions, such as those related to the collapse of spillway gates, are rarely studied. The objective of this study was to evaluate the effects of a rapid reservoir drawdown, because of the collapse of a gate, on the structure of fish assemblage in a Neotropical reservoir, in Southern Brazil, operated as run‐of‐the‐river. Water level variation because of the collapse reached up to 20 m. A canonical analysis of principal coordinates (CAP) was used to summarize the structure of fish assemblage. Spearman rank correlations were performed between each CAP axes retained for interpretation and fish species abundances, to assess the ones that most contributed to observed patterns. The first CAP axis identified strong variations in the spatial scale, while the third axis identified variations in the time scale (before and after the collapse). The most notable negative effect was the loss of several fish that perished during the reservoir drawdown, probably because of adverse limnological conditions. Results showed significant benefits of water level variation on the entire fish assemblage, and we suggest that, observed some peculiarities, this variation can be used to manage reservoirs, as a tool to enhance fish abundances. Copyright © 2016 John Wiley & Sons, Ltd.