Water shortage is a major problem that affects sustainability of agricultural sector in northeastern Thailand especially areas remote from a main river. This study aims at developing a system for water shortage risk assessment at sub-district level in Maha Sarakham Province. QSWAT model for sub-watershed streamflow simulation was integrated with WEAP model to analyze water balance and assess water shortage based on water demand from five sectors: non-irrigated agriculture, irrigated agriculture, consumption, services, and industry. The findings revealed that both models provided the results of calibration, and the validated results of streamflow analysis were at satisfactory to good level. From spatial analysis, distribution of provincial water resource was significantly different. Sub-districts located along the Chi River had high streamflow but low water shortage while those from central to southern part had limited streamflow although water demand was high especially for agricultural sector. According to temporal analysis, critical period of water shortage was found in the dry season and seasonal transition after post-harvest period. Integration of data on streamflow and water demand can be useful to divide subdistricts into three group: positive water balance, balance, and negative water balance. Most sub-districts were classified as negative water balance that needed urgent measures for water resource development. These findings have provided important data for planning water resource management locally and supporting development of drought mitigation measures for vulnerable areas in Maha Sarakham Province.