The effect of meteorological and hydrological droughts is very important in arid and semi-arid regions. So analyzing these effects on groundwater supplies play important role for managing water in those regions. Therefore, the aim of this paper is to characterize several kinds of droughts in Isfahan-Borkhar basin that is an arid area of Iran. Observed hydro-climatic data (for the period of 1971-2005) were used for hydro-meteorological projections (for the period of 2006-2040). Meteorological and surface hydrological drought evaluated by Standardized Precipitation Index (SPI), Standardized Runoff Index (SRI), and the effect of hydro- meteorological droughts on groundwater is investigated by Groundwater Resources Index (GRI). Results showed that dry and wet conditions would occur in the region in the initial and subsequent future decades, based on the three indices. There is an appropriate association between SPI, SRI, and GRI at the time scale of 12 months. The SPI estimated using only meteorological variables and better performed for meteorological drought forecasts than the SRI and GRI that computed using catchment discharge, soil moisture and groundwater level and represented hydrological drought. Results showed a considerable alteration of time of drought outlines across the area and association between the variables of predicted precipitation, temperature and the kind of indices. The projection of all three drought indices indicated drier conditions in the future period. The results provide reasonable management strategy for management of water resources in coastal plains.