Trace elements (TEs) contamination of agricultural soils requires suitable criteria for regulating their toxicity limits in soil and food crops, which depends on their potential ecological risk spanning regional to global scales. However, no comprehensive study is available that links TE concentrations in paddy soil with ecological and human health risks in less developed regions like Pakistan. Here we evaluated the data set to establish standard guidelines for defining the hazard levels of various potentially toxic TEs (such as As, Cd, Co, Cu, Cr, Fe, Mn, Ni, Pb, Se, Zn) in agricultural paddy soils of Punjab, Pakistan. In total, 100 topsoils (at 0–15 cm depth) and 204 rice plant (shoot and grain) samples were collected from five ecological zones of Punjab (Gujranwala, Hafizabad, Vehari, Mailsi, and Burewala), representing the major rice growing regions in Pakistan. The degree of contamination (Cd) and potential ecological risk index (PERI) established from ecological risk models were substantially higher in 100% and 97% of samples, respectively. The positive matrix factorization (PMF) model revealed that the elevated TEs concentration, notably Cd, As, Cr, Ni, and Pb, in the agricultural paddy soil was attributed to the anthropogenic activities and groundwater irrigation. Moreover, the concentration of these TEs in rice grains was higher than the FAO/WHO's safe limits. This study provided a baseline, albeit critical knowledge, on the impact of TE-allied ecological and human health risks in the paddy soil-rice system in Pakistan; and it opens new avenues for setting TEs guidelines in agro-ecological zones globally, especially in underdeveloped regions.