Small run-of-river hydropower plants (RRHPs) have revealed strong harmful effects worldwide on stream habitats (e.g., fragmentation and destruction) and decreased fish species, especially anadromous species abundance. Recently, RRHPs have rapidly been installed in Serbia. Most were installed on montane streams because their steep slopes are most convenient for hydropower energy production at minimal costs.Brown trout Salmo trutta are prominent in the fish communities of this rarest type of aquatic ecosystems. Their native molecular diversity reflects a biodiversity hotspot in the Balkans, and they provide attractive fishing opportunities. Records from fishery management plans for highland stream fisheries where RRHPs were installed revealed reduced brown trout biomass compared with streams without RRHPs.Research on six streams with operational RRHPs revealed severe deterioration of habitat, for example, increased water temperature, reduced dissolved oxygen, and increased nutrient contents. Effects on fish communities were evident from a change in their structure. Resident, stream-dwelling brown trout were the most affected species with steep declines in abundance, biomass, and productivity. Fragmentation owing to damming was also reflected by deterioration of their age structure. Unique native brown trout stocks susceptible to adverse effects are difficult to restore by stocking, and fish passages commonly supplied as compensation to overcome the disruption of habitats cannot mitigate the threat posed to the fish.