Trace metals pollution in the freshwater system is an emerging concern. Thus, a systematic study was performed in the Wadi Fatimah basin to appraise the trace metals pollution status, sources and associated health risks using integrated tools, namely indices, international standards, multivariate statistical techniques and health risk assessment models. The groundwater salinity shows a wide range (TDS = 391 to 11,240 mg/l). The heavy metal pollution index and contamination index justify that most of the samples are unfit for drinking due to high metal pollution. Severe pollution is noticed by the Li (100%), Ni (98%), Pb (86%) and B (78%), and it is in the decreasing order of Mo > Cr > Al > Fe = Mn > V > Sr > Ag > Cu. Pearson correlation matrix suggests that most of the metals have a significant strong positive correlation with Al, Fe and Mn and originated from geogenic sources. Principal components analysis and R-mode HCA indicate that trace metals are mostly derived from weathering of aluminium silicates, oxides/hydroxides of Fe and Mn followed by evaporation, evaporite dissolution and restricted flow. Q-mode HCA resulted in 4 clusters, and the water chemistry of WG1 and WG4 is governed by mineral weathering. In addition, evaporation also enriched the metal load and salinity in WG4 wells. In WG2, the water chemistry is predominantly affected by long storage, evaporation and mineral weathering. In WG3, the water chemistry is influenced by evaporation, irrigation return flow and evaporite dissolution. The hazard quotient and hazard index suggest that groundwater in this basin causes potential non-carcinogenic health risks to the consumer. This study strongly recommends treatment for groundwater before supply to the local inhabitants.