The present investigation attempted to understand the intensity, frequency and spatial coverage of rainfall, runoff, groundwater and agricultural droughts in the semi-arid region of Maharashtra during 1981–2014. For this, the SPI, SRI, SWI and SCPI indices of probabilistic nature were applied. The linear regression, partial correlation and Student’s t-Test techniques were also used to evaluate inter-connections in hydro-meteorological and agricultural droughts. The hydrological deficiencies mimic the pattern of meteorological droughts in the study area with respect to coverage and intensity. The frequency of moderate hydro-meteorological droughts is observed to be high (once in 3 to 4 years). The study also highlighted that the frequency and intensity of hydrological droughts were increased during the post-1990 period which perhaps associated with anthropogenic interventions. Although the El Niño events resulted in below-average rainfall, runoff and groundwater level in the study area, other phenomena such as EQUINOO/IOD may have played an important role in the occurrence of major droughts in 1986, 2003 and 2012 (occur once in > 30 years). The hydro-meteorological droughts lead to agricultural droughts, as the rainfall and groundwater deficits significantly affected the rainfed as well as irrigated crops (productivity and cropped area). It is notably observed during the severe and region-wide droughts in 1985-86, 2002-03 and 2011-12. Furthermore, this investigation suggested that the study area is very likely to experience hydro-meteorological deficiencies in 2029-30, 2040 and 2050 along with a significant rise in temperature (by 1.05°C) which will exacerbate the water scarcity and agricultural distress in the future (up to 2050).