Hydropower production leads to losses of species and ecosystem types in rivers. A major knowledge gap is represented by bypassed reaches where all or most discharge is diverted to hydropower stations. Bypassed reaches may have some flow, derived from tributaries and dam leakage, along with minimum flow. In Sweden, mandates for minimum discharge are lacking for most bypassed reaches, and when present, generally amount to only a few percent of mean annual discharge. We asked how fish communities in bypassed reaches differ from comparable non-regulated reference reaches, and whether minimum discharge can help sustain fish faunas typical of non-regulated rivers. We assembled a unique dataset of 2693 samples collected via electrofishing by wading from 166 bypassed reaches and 247 free-flowing reaches spread across Sweden. To quantify flow-related community changes, we compared the relative dominance of rheophilic (preference for high flow conditions) versus limnophilic (preference for slow-flowing to stagnant conditions) fish species, fish density, and fish species richness between bypassed and free-flowing reaches, and investigated the effects of minimum discharge on community structure. Bypassed reaches had lower rheophilic dominance and fish density, but slightly higher fish species richness than comparable free-flowing reaches. Minimum discharge had positive effects on rheophilic dominance and fish density but not fish species richness. For relatively low values of minimum discharge, small changes in flow corresponded to large changes in the predicted values of fish density (up to about 0.5 m³/s) and rheophilic dominance (up to 2 m³/s), after which curves flattened. When minimum discharge was expressed as a percentage of mean annual discharge, rheophilic dominance and fish density increased almost linearly with increasing discharge, but effects on fish density were dependent on river size. We conclude that small increases in minimum discharge can be particularly beneficial to the restoration of rheophilic community structure, especially at low levels of minimum flow, even though the area of lotic habitat has been reduced to a fraction of natural conditions. Implemention of minimum discharge in bypassed reaches can thus be an effective rehabilitation measure, providing ecological benefits helping to meet environmental objectives.