Kazakhstan has been experiencing water scarcity due to high inter- and intra-annual precipitation and streamflow variability, which adversely impacts the country’s agricultural production and economy. In order to design suitable adaptation measures, a detailed analysis of characteristics and trends in climate data is essential. This study analyses recent climate data (1981–2019) and global gridded datasets on water balance components for two Kazakh regions. The data was analysed using Mann–Kendall trend test, extreme precipitation indexes, analysis of wet/dry spells and droughts. The results indicate that while the average annual precipitation amounts were not significantly different between the regions, there was a distinct intra-annual variability. Significant trends in hydroclimatic variables appear in the south during winter and spring, and in the north mainly in spring. No significant trends are observed for extreme precipitation. Evapotranspiration controls the water balance in both regions. Potential water available for groundwater recharge is higher in the north. Snowpack in the south is highly variable and shows a significant decreasing trend. Based on the results, managed aquifer recharge (MAR) is proposed as a potential solution to enhance water availability throughout the year, leveraging the highly variable precipitation and streamflow patterns. In both cases, the irregularly available water resources, such as spring snowmelt and heavy summer rains, can be stored through MAR schemes, thereby providing reliable support to water supply systems. This approach can serve as a countermeasure to the recurrent dry spells and droughts in the region, as well as to the climate-induced alterations of the local water balance.