The paper presents long-term changes in water temperature in two rivers, Oder and Neman, with catchments showing different climatic conditions (with dominance of marine climate in the case of the Oder and continental climate in the case of the Neman River). A statistically significant increase in mean annual water temperature was recorded for four observation stations, ranging from 0.17 to 0.39 °C dec−1. At the seasonal scale, for the winter half-year, water temperature increase varied from 0.17 to 0.26 °C dec−1, and for the summer half-year from 0.17 to 0.50 °C dec−1. In three cases (Odra-Brzeg, Odra-Słubice, Niemen-Grodno), the recorded changes referred to the scale of changes in air temperature. For the fourth station on Neman (Smalininkai), an increase in water temperature in the river was considerably slower than air temperature increase. It should be associated with the substantial role of local conditions (non-climatic) affecting the thermal regime in that profile. Short-term forecast of changes in water temperature showed its further successive increase, a situation unfavorable for the functioning of these ecosystems.