River discharge has experienced diverse changes in the last decades due to modification of hydrological patterns, anthropogenic intervention, re‐vegetation or annual and interannual climatic and atmospheric fluctuations. Assessing the recent changes in river discharge and understanding the main drivers of these changes is thus extremely important from theoretical and applied points of view. More specifically, here we want to draw attention toward the impacts of streamflow changes on reservoir storage and operation. We describe the hydrological dynamics of the Yesa reservoir draining catchment, located in the central Spanish Pyrenees, and characterize the reservoir operation modes over the last 60 years (1956–2020). We analyze concurrent climatic (precipitation, air temperature, drought index), atmospheric mechanisms, land cover (Normalized Different Vegetation Index) and discharge (inlet and outlet of Yesa reservoir) time‐series. By using the wavelet transform methodology, we detect historical breakpoints in the hydrological dynamics at different time‐scales. Distinctive periods are thus identified. More regular seasonal flows characterized the catchment's dynamics during the first decades of the study period, while the last decades were characterized by a high inter‐annual variability. These changes are primarily attributed to the natural re‐vegetation process that the catchment experienced. Furthermore, we related changes in atmospheric circulation with a decline of the long‐term discharge temporal features. This research contributes to the understanding of long‐term river discharge changes and helps to improve the reservoir management practices. Key Points Incoming river flow to Yesa reservoir dwindled as vegetation cover increased Inter‐annual time‐scales increased their control of the annual discharge The is a growing influence of Mediterranean atmospheric dynamics on the river flow discharge