Study Region: The Thaya river basin provides multiple water uses in the transboundary region of Lower Austria and Southern Moravia. Due to the low precipitation (P) to reference evapotranspiration (ETo) ratio, the Thaya river basin is among the most sensitive to climate change in the region. Study Focus: The main objective is to understand the changes in the water balance variables including actual evapotranspiration (ET), P and runoff (RO) and their drivers for the period 1981–2020, and 2001–2020 in the case of using remote sensing data. New Hydrological Insights for the Region: The analyses confirm previously reported increasing trends in air temperature, ETo, and no trends in P. ET consistently increased during spring and decreased during summer, although insignificantly. This change was associated with a significant increase of spring vegetation development followed by summer stagnation. The spring RO shows significantly decreasing trends, especially in the upland water source areas. The correlation analysis reveals a different behavior along the altitude gradient, with ET in the uplands generally limited by available energy whilst in the lowlands by available water in spring. In summer, however, the entire basin is often water-limited, with a more pronounced limitation in the lowlands. Complex adaption measures reflecting the different hydroclimate relations across the altitudinal gradient are needed to sustain the water dependent sectors operating in the region facing increasing aridity.