Several previous studies have examined the traceable regional impacts of El Niño Southern Oscillation (ENSO) on groundwater level (GWL) but it remains a question whether the ENSO impacts on groundwater can be established in smaller basins using statistical techniques. The present study attempts to record the ENSO impacts on the groundwater availability in Venna basin, Maharashtra by proposing a combination of statistical and spatial analysis. Utilizing the GWL, the study estimates the spatial variability of GWL, groundwater anomalies, groundwater recharge and discharge using geographic information system (GIS) and quantitative variations in groundwater using statistical techniques. The study also highlights the applicability of the Kolmogorov–Smirnov test in hydrometeorological studies. Analyses reveal the association of deeper GWLs and higher discharge with the El Niño, as opposed to shallower GWLs and higher recharge with La Niña. The two-sample Kolmogorov–Smirnov test confirms the discrepancy in the cumulative distribution of GWL between different ENSO phases. Mann–Kendall, Sen slope and Mann–Whitney tests ascertain the variation of GWL and recharge as well as ENSO impacts in the command area (area irrigated by reservoir using the canal networks) and non-command areas. A significant difference in recharge between El Niño and La Niña is observed in the command as well as in the non-command areas.