The transboundary Prut River basin (PRB) is one of the most drought vulnerable areas in the Republic of Moldova, Romania, and Ukraine. The main objective of this study was to identify the response of hydrological drought to climatic conditions and cropping practice in a region with insufficient water resources. The presented work takes advantage of the development of statistical tools to analyze existing data, as well as the collection of qualitative and quantitative hydroclimatic datasets for each sub-basin region. The study also provides survey results of the impacts of climate change on agricultural water management, including agricultural water requirements and water availability, and the transition of these impacts to cropping practice. The multi-dimensional attributes of hydrological drought are defined according to the standardized streamflow index (SSI) and water-level standardized anomaly index (SWI). The standardized precipitation evapotranspiration index (SPEI) was selected for the assessment of the impact of climate drought control on hydrological drought. The streamflow/water river level is determined more by the climatic water balance deficit of the previous 6 months than over longer periods. The lag times between climatic and hydrological drought are short, which can cause a hydrological drought to occur in the same season as the climatic drought that caused it. Summer streamflow droughts are most closely linked to SPEI in the same month. Summer streamflow drought in upstream areas can impact streamflow at the outlet within the same month. Winter streamflow droughts are related to longer SPEI accumulation periods resulting from snow cover. The synthesis of findings from the river basin shown that concurrent compound climate events have much more severe impact on crop failures compared to their individual occurrence. Adjustments to sowing time (15%), the introduction of more drought resistant cultivars (11%), the use of crop protection measures (9%), and shifting to new crops (8%) seem to be minor and moderate adaptation practices employed by farmers.