Most studies of brown trout (Salmo trutta) populations in headwater streams have focused on the year-to-year variability in recruitment and survival, but only few analyzed long-term trends in trout densities, under both control and regulated flow conditions. Here, we conducted trend analyses of brown trout age class densities on 36 stream reaches over the 1990-2020 period, including reaches located in a bypassed section. We also investigated long-term trends in a panel of key environmental variables (water temperature, stream flow, current velocity and habitat suitability). We found that annual water temperatures significantly increased by a median of +0.21 °C per decade. Analyses of stream flow revealed only a few significant trends, including a general increase in median values in spring and a general decrease in fall. A significant general decline in adult trout densities was observed, although disparities between geographic areas were highlighted. This decline is likely due to multifactorial effects, including possible interacting factors. Our results highlight the need to maintain and extend long-term monitoring of trout populations, which should be combined with extensive environmental monitoring.