Thermal alteration is one of the adverse effects of flow regulation sharpened in recent years due to climate changes. In this work, we characterize the thermal regime of a highly regulated river located in Northern Italy, which is the emissary of Lake Maggiore. The thermal characteristics of the study reach are influenced by the presence of two dams and by climate warming. In the 15-year monitored period (1999-2013) a significant increase of the mean annual river temperature (i.e., +1.8°C) was indeed recorded. Minimum and maximum water temperatures were detected in correspondence of low-flow periods in February and August, respectively. During August the temperature reached a maximum of 27°C, that is a value below the upper thermal limit of tolerance for most of the aquatic taxa collected in the study area. Moreover, the local presence of seeps and the interaction with groundwater play an important ecological role by guaranteeing patches of cool water to the aquatic communities. Nevertheless, the sensitive early life stages of fish species that spawn in spring/summer may be affected by the high summer temperatures and the expected future climate warming. The wider range of temperatures preferred by alien fish species could result into a competitive disadvantage for autochthonous species. The current minimum flows established by local laws as environmental flows appeared to be able to guarantee an acceptable thermal alteration in morphologically heterogeneous reaches where river/groundwater interaction occurred, at least within the current climatic conditions.