Pakistan is an agricultural and developing country. The use of wastewater to irrigate agricultural farms is increasing day by day due to water shortage in the country. This study assessed the Potential Ecological Risk Index (PERI) of soils of agricultural farms (six sites) being irrigated with industrial effluents, urban sewage, canal and tube-well water in suburb of Multan city, Pakistan. Surface soil samples (n = 30) from the six sites were analyzed for cadmium (Cd), chromium (Cr), copper (Cu), manganese (Mn), nickel (Ni) and lead (Pb) by inductively coupled plasma-optical emission spectrometry (ICP-OES). Samples of wastewater/water (n = 30) used for irrigation from respective sites were analyzed for same metals for statistical analysis. Mean contents (mg/kg) of Cd (5.65), Cr (153.1) and Pb (63.95) in soil under industrial effluents exceeded the threshold limits. The ecological risk factor 5650 > 320 for Cd was the highest and contributed 91-98.6% in raising the ecological risk. Cd, Cr, Cu and Pb were the prominent contaminants in soil across all sites. Soil under industrial effluents showed very high ecological risk (PERI 5730>600) and soils under urban wastewater exhibited moderate risk (PERI 153.5–294) and soils under tube well and canal water indicated low risk (PERI 138–149.7<150). Statistical analysis indicated that soil contamination is sourced from wastewater and water applied for irrigation is. Very high and moderate ecological risk of soils are source of food chain contamination. Proper treatment of wastewater before its use in agricultural farming system may save the health of ecosystem.