Groundwater contamination due to the disposal of untreated or partially treated domestic and industrial sewage is posing a severe threat to urban groundwater reserves in many parts of the world. The efforts made for the modelling of contaminant transport to understand these pollution transport and hydrogeochemical processes in urban areas are often challenging due to the difficulty in selecting source boundary condition locations mainly in the presence of Multiple Point Sources (MPS). The present research used Multivariate Statistical analysis (MSA) to classify the major pollution sources and to demarcate its area in the highly urbanized Hussain Sagar (HS) lake catchment situated in Hyderabad, South India. The observed monitoring data of groundwater levels and groundwater quality (pH, TDS, Ca2+, Mg2+, Na+, K+, HCO32−, Cl−, SO42−, NO3-N, total hardness) at 108 locations for eight different seasons over four years have been used for modelling. The MSA has revealed that the first component is associated with industrial pollution loads that are restricted to Kukatpally and Dulapally streams and HS lake with a total variance of up to 46% to the total pollution load. Component 2 and component 3 are associated with domestic pollution loads (HCO32−, Na+, and NO3-N) that spread across the lake catchment with a total variance of up to 37%. The approach used in this study can be applied to any local to regional scale river basins for understanding hydrogeochemical processes and to provide inputs to simulate contaminant transport.