Droughts have been poorly studied in Estonia despite of the important water deficit that occurred in recent times e.g. 2002 and 2006. We have studied the influence of atmospheric indices on the spatial and temporal variability of droughts in Estonia. We have analyzed 57 monthly precipitation series and 7 atmospheric indices (NAO, EA, EATL/WRUS, SCAND, P/EU, AO and WI) during the period 1951-2015. Estonia has been regionalized in three homogeneous regions according to drought variability, i.e. western, southeastern and northern. Standardized precipitation index at timescale of 1, 3, 6, and 12 months have been computed for each region. From 1951 to 1977 dry conditions prevail. On the other hand, from 1978 to 2015 wet conditions prevail interrupted by some intense but short droughts. The main influence of atmospheric indices on drought variability is recorded with SCAND for spring and autumn (negative correlations) and with WI for winter and summer (positive correlations).