Groundwater is the dominant source of freshwater in many countries around the globe, and the deterioration in its quality by contaminants originating from anthropogenic sources raises serious concern. In this study, a scenario where groundwater is contaminated by acid mine drainage (AMD) from mining activities and/or sewage was envisaged, and the performance of a direct contact membrane distillation (DCMD) system was investigated comprehensively for different compositions of the AMD- and sewage-impacted groundwater. Regardless of the composition, MD membrane achieved 98–100% removal of metals and bulk organics, while the removal of the selected micropollutants ranged between 80 and 100%. Effective retention of contaminants by the MD led to their accumulation over time, which affected the hydraulic performance of the MD membrane by reducing the permeate flux by 29–76%. When persulfate (PS)-mediated oxidation process was integrated with the DCMD, degradation of bulk organics (50–71%) and micropollutants (50–100%) by PS reduced their accumulation. Characterisation of the fouling layer revealed the occurrence of membrane scaling that was mainly due to the deposition of iron oxide or oxyhydroxide precipitates. For an identical composition of the AMD- and sewage-impacted groundwater, flux decline was 10% less in PS-assisted DCMD as compared to that in the standalone DCMD. However, this did not prevent the formation of iron oxide scales on MD membrane during the operation of PS-assisted DCMD. This study demonstrates the long-term performance of a standalone and PS-assisted DCMD operated in continuous-flow mode to treat AMD- and sewage-impacted groundwater for the first time.