Geochemical baseline (geogenic+anthropogenic) and background (geogenic) levels of heavy metals in the ground waters from basaltic aquifers of Deccan Volcanic Province of India depicted intra-annual variability on spatial scale. Classified into ‘Group I’ (Fe > Mn > Zn > Pb) and ‘Group II’ (Mo > Ni > Cr > Cu), metals depicted contrasting enrichment and depletion patterns seasonally, attributable to geologic controls and water table fluctuations. While, fortification in Mo–Ni in post-monsoon (high water table) is on account of combined lithogenic+anthropogenic contributions, pre-monsoon augmentation in Fe–Mn (low water table) is entirely lithogenic. Positive values of Normalised Difference Dispersal Index, replicates the dominant role of soil/vadose zone as a chief supplier of metals to the groundwater during post-monsoon, while negative figures recommend host rock as a primary source of accretion of metals in pre-monsoon. Higher Ni/Cr ratios for wells in alluvial aquifer (fertile agriculture plain) than the basaltic and dyke aquifers, further suggest enhanced input of the elements (Mo, Ni > Cu) from soil and agriculture land use in post-monsoon season. Values of Ni/Cr ratio above unity for majority of the wells in post-monsoon and nearly 50 % wells in pre-monsoon suggest privileged weathering of olivine, followed by pyroxene > plagioclase feldspar (Ni/Cr <1) as a major cause of heavy metal load to the groundwater. Pearson correlation coefficients authenticate these inferences by means of elemental associations. The study unveils multi-source derivation of heavy metals related to seasonal fluctuation in the water table conditions leading to range of heavy metals in the groundwater from the study area. The target hazard quotient (THQ) values of heavy metals closer to unity and above unity highlight the possible health risk hazard associated with the consumption of metal contaminated groundwater. The study thus highlights the importance of baseline geochemical mapping to assess the state of near surface environment as heavy metals are closely linked to human health.