Abstract Salmonids inhabiting Mediterranean rivers are of particular concern for biodiversity conservation, as they are threatened by various stressors, including habitat alterations, overfishing, climate change, and introgressive hybridization with alien species. In the Tiber River basin (Central Italy), genetic introgression phenomena of the native Salmo cettii with the non‐native Salmo trutta hinder the separate analysis of the two species, which are both included in the S. trutta complex. Little is known about the factors currently limiting the trout populations in this area, particularly with respect to climate change. With the intention of filling this gap, the aims of the current study were to (a) quantify changes in the climate and (b) analyze the distribution, status, and ecology of trout populations, in the context of changing abiotic conditions over the last decades. Fish stock assessments were carried out by electrofishing during three census periods (1998–2004, 2005–2011, and 2012–2018) at 129 sites. The trend over time of meteorological parameters provided evidence for increased air temperature and decreased rainfall. Multivariate analysis of trout densities and environmental data highlighted the close direct correlation of trout abundance with water quality, altitude, and current speed. Climate‐induced effects observed over time in the sites where trout were sampled have not yet led to local extinctions or distribution shifts, indicating a marked resilience of trout, probably due to the buffering effect of intrinsic population dynamics. Decreasing body conditions over time and unbalanced age structures support the hypothesis that variations in hydraulic regime and water temperature could overcome these compensatory effects, which may lead to a severe decline in trout populations in the near future. In a climate change context, habitat availability plays a key role in the distribution of cold‐water species, which often do not have the possibility to move upstream to reach their thermal optimum because of water scarcity in the upper river stretches.