Industrial and domestic wastewater is a potential contaminant capable of degrading the quality of the soil environments, if not properly treated. This study reports the 20 years cumulative effects of treated wastewater discharge on heavy metal (HMs) concentration in the proximal environment of Palapye Wastewater Treatment Plant (PWTP), Central Botswana. Soil samples were collected from eight sites: four along the treated wastewater channel and four on an adjacent well-drained channel (control). Selected physico-chemical properties of the soils were determined using routine laboratory procedures and rapid HM concentrations with portable XRF. Results showed that HM concentrations in the two drainage classes did not vary significantly (p > 0.05). There was strong correlation between organic matter (OM) and Fe (R-2 = 0.896, p < 0.01), OM and Cu (R-2 = 0.908, p < 0.01), OM and Zn (R-2 = 0.956, p < 0.01) and OM and Mn (R-2 = 0.954, p < 0.01) in control soils, while treated wastewater affected soils showed strong correlation for OM and Fe (R-2 = 0.765, p < 0.01), OM and Zn (R-2 = 0.770, p < 0.01) and OM and Mn (R-2 = 0.802, p < 0.01). Source apportionment of HMs using PCA shows one component in the control soils accounted for 77% of the total variance, while two components accounted for 97% of the total variance in treated wastewater affected soils. The geoaccumulation (Igeo) and pollution load (PLI) indices used to assess potential pollution show all soils to be unpolluted. Manganese which showed enrichment at two sites might indicate possible pollution, but their speciation and bio-accessibility, rather than total concentrations, have to be established.