Effective protection of migratory fish requires long‐term conservation encompassing active restoration and management measures with follow‐up studies. The main findings of long‐term (1995–2019) monitoring of anadromous and potamodromous brown trout Salmo trutta in the River Bidasoa are presented. The main aims were evaluating trout number and median migration date changes, and assessing the effects of management (closures, size limits and quotas, fish stoking) and connectivity measures (fishways and weir removals). Results showed an increasing trend in upstream migrants and decrease in migration dates (earlier migrations). Effects of overlapping measures were difficult to differentiate and were affected by environmental conditions. Statistical analysis demonstrated that fishing closures (2008–2011) and fishway construction (2008) were of great importance, whereas the effect of fish stocking (2003–2012) was variable and unclear. The unexpectedly short‐term effect of three weir removals (2014–2016) may have been due to unusually high discharges in March, affecting the recruitment during previous years.