Alterations of natural hydrology in aquatic ecosystems are known to strongly impact the community composition of different taxa. Surprisingly, literature on the potential influence of hydrology on fish community composition is still very scarce in agricultural marshes, where canals represent one of the few remaining aquatic habitats. This study is aimed to address this research gap by monitoring fish communities in independent hydrological units differing in hydrology management over a 6 years period. We predicted variable fish responses to the hydrological context according to different life-history strategies (opportunistic, equilibrium, or periodic species). Periodic and opportunistic species were the most frequently observed. Despite differences in hydrology between canals (but little variation over years), we found that hydrology explained only a very low proportion of variation in the composition of fish communities. In particular, the flooding duration of meadows in early spring did not influence the composition of fish communities, not even the abundance of periodic species expected to rely on such temporary habitats. Instead, fish communities were more influenced by local habitat variables (aquatic vegetation cover, turbidity, tree roots, and refuges under the canal banks). The hydrological management of most hydrological units for agricultural purposes (i.e., severe flood abatement in spring and shallow water depth in canals in summer) was found to be incompatible with conservation goals to promote more diverse fish communities between hydrological units. Therefore, we call for further investigations in similar habitats covering a larger range of hydrological conditions.