At the beginning of the 21st century, ongoing climate change led to research into extreme streamflow phenomena. This study aimed to assess the patterns of low-flow changes in different hydrological regions of Lithuania using selected hydrological indices (the annual minimum 30-day flow (m3 s−1) of the warm period—30Q), its duration, and deficit volume (below the 80th and 95th percentile flow: 30Q80 and 30Q95). Differences in low-flow indices in separate hydrological regions and over different periods (1961–2020, 1961–1990, 1991–2020) were analyzed, applying the HydroOffice tool, the TREND software package, and mapping using the Kriging interpolation. The highest specific indices of 30Q were estimated in the Southeastern hydrological region (3.97 L/s·km2) and the lowest in the Central hydrological region (1.47 L/s·km2). In general, the 30Q values in the periods 1961–2020 and 1991–2020 had no trends. In 1961–1990, trends in 30Q data were significantly positive, and positive in most investigated rivers of the Western and Central hydrological regions. The average number of dry days at both thresholds decreased in the Western and Southeastern hydrological regions and increased in the Central hydrological region comparing two subperiods.