This study used multivariate analysis and geochemical modeling to appreciate the trace element evolution in North Rukuru–Songwe alluvial aquifer of northern Malawi. From the isotopic studies, the δ2H/δ18O ratios revealed that groundwater is of meteoric origin through vertical recharge and mixing processes. The isotopic depletion along the west–east transect is due to mixing and fractionation processes. Generally, the d-excess value approximated the y-intercept of global meteoric water line of 10, which ruled out the influence of secondary evaporative processes on isotopic variation. Hierarchical cluster analysis identified four distinct clusters (C1, C2, C3 and C4) in the study area. Among these four clusters, it was observed that C1 had relatively high median concentrations of Fe (716.7 µg/L), Cr (0.85 µg/L), Pb (7.90 µg/L) and Sb (3.80 µg/L), while C2 was characterized by high levels of Cu (3.20 µg/L). Cluster 3 was comparably defined by high median levels of F (1.00 mg/L) and Mn (338 µg/L), while C4 revealed high median concentrations of As (8.70 µg/L), Ba (635 µg/L), Li (22.2 µg/L), Ni (2.80 µg/L), Se (6.20 µg/L) and Sr (677 µg/L). Clusters C1 and C4 described a flow path along the North Rukuru River, which is characterized by higher levels of evaporites as shown by higher concentrations of Na, K, Cl and SO4. It was also observed that this path was defined by high levels of HCO3 and total hardness. The principal component analysis suggests that carbonate dissolution and silicate weathering are the main mineralization control mechanisms. Furthermore, it is revealed that samples in the west had higher factor scores for As, Ba, Li, Ni, Se and Sr (with higher TDS), while the eastern is characteristic of higher heavy metals (Fe and Pb). Geochemical modeling using PHREEQC showed that surface complexation reactions significantly impact trace elements of higher redox state. In addition, inverse modeling confirms the significance of carbonate dissolution, silicate weathering and cation exchange processes along the North Rukuru River flow path.