Water management strategies in the Ile River basin (Republic of Kazakhstan) have traditionally relied on historical data without fully considering the potential impacts of climate change. This gap can lead to underestimating the changes in temperature, precipitation patterns, and runoff, hindering effective water resource management. This study aimed to analyze how a changing climate is affecting the Ile River basin’s water regime. Specifically, it investigated trends in temperature, precipitation, and runoff within the basin, emphasizing the importance of incorporating these intra-annual variations when planning water management strategies and hydraulic structures. A detailed analysis of the long-term data was conducted, focusing on changes in meteorological indicators. This included average air temperatures and annual precipitation for elevations above and below 1500 m during cold and warm periods. The analysis aimed to identify and quantify trends of increase or decrease. Meteorological stations were strategically chosen to represent both arid and humid areas within the basin, accounting for the region’s significant altitude variations. The investigation revealed several key findings. Rising average annual air temperatures are leading to a larger area experiencing snowmelt and a longer warm period within the runoff formation zone. This directly impacts the water balance of the basin. Additionally, an increase in total annual precipitation, particularly during the cold season within the runoff formation zone, suggests a potential for future water resource growth, assuming that these trends persist. This study highlights the importance of considering intra-annual variations in water regimes when developing water management strategies. The observed changes in temperature and precipitation patterns within the Ile River basin necessitate adjustments to existing plans to ensure sustainable water resource management in a changing climate.