Hydropeaking dam operation and water extractions for irrigation have been broadly stated as alterations to natural flow regimes, which have also been noticed in the Biobío Watershed, in Central Chile, since 1996. In the Biobío River, most of native fish species are endemic and very little is known about them. Their ecological and social values have never been estimated, and there is lack of information about their habitat preferences. Furthermore, changes on fish habitat availability due to natural and/or man-made causes have not been evaluated. In this study, eight native fish species, in a representative reach of the Biobío River, were studied and their preferred habitats were surveyed and characterized. A hydrodynamic model was built and linked to the fish habitat simulation model CASiMiR. Fuzzy rules and fuzzy sets were developed for describing habitat preference of the native fish species. CASiMiR was then used to simulate how physical habitat conditions vary due to flow control (i.e. upstream dams). Results show how overall habitat quality, expressed as weighted usable area (WUA) and hydraulic habitat suitability (HHS), changes and fluctuates due to the dam operation and how the daily hydropeaking is influencing quantity, quality and location of different habitats. The study suggests that the analysed fish are highly susceptible to flow control, as dams are currently operated, and fish habitat improvement suggestions are proposed.

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The magnitude of hydropower developments in emerging regions threatens the sustainability of their riverine landscapes. Fragmentation of river networks by multiple barriers and the imposition of new hydrological regimes influences the ability of these river ecosystems to absorb and adapt to these developments and other stressors. Direct transfer of paradigms built from a restricted geographical base to a global context is fraught with issues because of regional differences in eco‐hydro‐geomorphology, biological communities, and nonlinear interactions between the two. In this manuscript, some impacts of hydropower development on Chilean riverine ecosystems are presented. To understand the context of hydropower, we provide the political context of energy development in Chile. Interactions between hydropower generation and Chilean river ecosystems with special reference to native Chilean fish fauna are outlined. Three case studies are presented that considers: (a) habitat alteration downstream of the Rucúe Dam, (b) the effects of daily hydropeaking in the Biobío River, and (c) mitigation strategies to reduce habitat alteration upstream of the San Pedro Dam. These case studies illustrate the expanding scientific knowledge on Chilean riverine landscapes. Finally, new measures to reduce ecosystem impacts of hydropower development on native Chilean fish communities are outlined. Although specific scientific information is available, developing regional ecohydrological models and improving knowledge of ecosystem and sustainability science is required. The scientific approach on which solutions are sought to address present and future river ecosystem problems in Chile are inherently interdisciplinary nature.

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