This article provides a comprehensive analysis of long-term changes in the minimum river flow of the southern rivers of Western Kazakhstan (Temir, Oiyil, Zhem) for the period 1940-2022, with an emphasis on summer minimum and winter low flow as key indicators of water and environmental sustainability in conditions of increasing climate variability. The study combines a typology of the climate control mechanisms of minimum flow, analysis of structural homogeneity, and assessment of the internal organization of time series based on ITA and the integral IPTA method, which allow us to reveal the hidden fluctuations and stable phase states of the hydrological regime. The calculation of the climate sensitivity index (CSImin) showed pronounced seasonal asymmetry: summer runoff is largely controlled by atmospheric precipitation, while winter minimum runoff is determined by temperature regime and soil freezing depth. Parametric and nonparametric tests (Pettitt, ADF, SNHT) revealed significant structural shifts in the 1960s-1990s period, corresponding to large-scale climatic anomalies in the region. Summer series are characterized by phases of prolonged low water levels and negative trends in the mid-20th century, while for the winter period, a steady increase in minimum flow has been established, due to regional warming and an increase in the share of underground recharge. IPTA confirmed the presence of long-term phases with high internal heterogeneity in the summer season and a more stable winter runoff structure. The results demonstrate the high climatic sensitivity of minimum runoff and confirm the need to move from static standards to dynamically adaptable methods of water resource assessment. The proposed approach can serve as a tool for developing adaptation strategies, assessing the risk profile of basins, and improving the sustainability of water management planning in arid regions.