Improving the environmental quality of effluent‐dominated seasonal rivers is a fundamental challenge for sustaining life in drylands, where people utilize contaminated water to produce food, which ultimately accumulates in the food chain. Preventing further contaminations and phytoremediation are needed to avoid environmental degradation and health risks. This study aimed at analysing water quality and its impacts on soil and vegetation at effluent‐impacted, river‐edge and non‐polluted (control) micro‐habitats at five sites along Luni, Bandi and Jojari Rivers each in western Rajasthan. Soil and water samples were collected and analysed, and vegetation was recorded. River water exhibited high pH (7.60–8.60), electrical conductivity (EC; 2.45–38.20 dS m−1), total dissolved solid (TDS; 1.26–30.86 g L−1), alkalinity (24.0–250.0 mg L−1) and Na (1.50–30.00 g L−1), K (29.0–1100.0 mg L−1), Ca (136.0–3800.0 mg L−1) and Mn (0.05–83.92 mg L−1) concentrations and low NH4‐N, NO3‐N, PO4‐P and heavy metals. Species numbers ranged between 32 along Luni and 20 along Jojari. Soil pH, EC, PO4‐P and shrub richness (R), diversity (H′) and evenness (e') were highest for Bandi, whereas NH4‐N, NO3‐N, K and tree R and H′ were highest for Jojari River. Soil variables decreased and plant diversity increased downstream. Concentrations of Cd, Zn, Cr, Cu and Pb were above the acceptable limit in leaf of Salvadora persica and Prosopis juliflora. Principal component analysis (PCA) revealed significant relationships between different variables of river water, soil, and vegetation and 11 PCA axes. Conclusively, industry effluents negatively affected water, soil and river ecology. Effluent‐impacted soils had high salinity and less diversity adapted by salt‐tolerant species, complementary effects of which contribute to restoring the modified ecosystem and urban greening. Although people utilize effluent‐contaminated water in irrigation, precautions should be taken to avoid environmental and animal/human health risks.
