The sustainability of rural areas depends on the availability of water resources. The Mangyeong River Basin (MRB) in Korea faces a water supply shortage for agriculture and industry. Based on 11-year (2005–2015) precipitation and groundwater monitoring data, groundwater sustainability was evaluated in terms of natural and man-made factors and their spatio-temporal variations. A precipitation time-series revealed a declining trend, but there were different seasonal trends between wet and dry periods, with declining and rising trends, respectively. Groundwater hydrographs from five national groundwater monitoring wells showed temporal variations. Groundwater wells located in downstream areas showed both recharge from upgradient areas and local man-made impacts (e.g. from pumping), resulting in an ambiguous relationship between precipitation and water levels. However, other monitoring wells in the upstream areas displayed water level responses to precipitation events, with a declining trend. Using the standardized precipitation index at a time scale of 12 months (SPI-12) and the standardized groundwater level anomaly, meteorological and groundwater drought conditions were compared to infer the relationship between precipitation deficit and groundwater shortage in the aquifer. The SPI results indicated severely dry to extremely dry conditions during 2008–2009 and 2015. However, the standardized groundwater level anomaly showed various drought conditions for groundwater, which were dependent on the site-specific hydrogeological characteristics. Finally, groundwater sustainability was assessed using water budget modelling and water quality data. Presently, if groundwater is used above 39.2% of the recharge value in the MRB, groundwater drought conditions occur throughout the basin. Considering water quality issues, with nitrate being elevated above the natural background, this critical abstraction value becomes 28.4%. Consequently, in the MRB, sustainable groundwater management should embrace both natural and human-induced factors to regulate over-exploitation and prevent contamination.