Discriminant analysis (DA) was performed on river hydrochemistry data for three seasons (i.e., monsoon (MON), post-monsoon (POM), and pre-monsoon (PRM)) to examine the spatio-temporal hydrochemical variability of two mountain river basins (Muthirapuzha River Basin (MRB) and Pambar River Basin (PRB)) of the southern Western Ghats, India. Although the river basins drain tropical mountainous terrain, climate and degree of anthropogenic disturbances show significant differences (i.e., humid, more disturbed MRB vs semiarid, less disturbed PRB). In MRB, TDS, Na(+), pH, Mg(2+), and K(+) are the attributes responsible for significant hydrochemical variations between the seasons, while Cl(-), TH, and Na(+) are the predictors in PRB. The temporal discriminant models imply the importance of rainfall pattern, relative contribution of groundwater toward stream discharge and farming activities in hydrochemistry between the seasons. Inclusion of hydrochemical attributes (in the temporal discriminant functions) that can be derived from both natural and anthropogenic sources suggests that ionic enrichment strongly depends on the seasons, and is mainly due to the variability in the intensity of anthropogenic activities as well as fluctuations in river discharge. In spatial discriminant models, Cl(-) is the only variable responsible for hydrochemical variations between the basins (during MON), whereas Si discriminates during POM and PRM, implying the role of atmospheric supply, anthropogenic modifications as well as intensity of weathering. In the spatial discrimination models, misclassification of hydrochemistry data between MRB and PRB can be attributed to the overlapping effect of humid climate of MRB extending toward the upstream of (semiarid) PRB. This study underscores the versatility of DA in deciphering the significance of climatic controls on hydrochemical composition of tropical mountain rivers.