Quality and quantity of different irrigation water types from conventional and alternative sources have a significant role on the productive parameters and chemical composition of crop plants. Appropriate alternative water sources and the reutilization of agricultural effluents can reduce the impact of rice production and animal husbandry on the natural water bodies. In the present study, influence of four different types of irrigation water was analyzed on the nutrient uptake (P, K, Ca, Mg, Na) of aerobic rice (Oryza sativa L.) in a complex lysimeter experiment in two consecutive years. Early maturing Hungarian rice varieties (M 488 and Janka) were irrigated with traditional river water (RW) and different alternative irrigation sources to evaluate the feasibility of a sodium containing intensive fish farm effluent with (EWG) or without (EW) gypsum supplementation and with the addition of natural river water (EWGR). Significant effects on the mineral content of the aboveground biomass were measured. P uptake by M 488 and Janka decreased after the irrigation with EW in 2017. In case of EW, EWG and EWGR, the Na content increased significantly (p ≤ 0.05) in both varieties; however, pre-treatment of salt containing effluent waters can moderate the stress level. As a consequence, the ability of both rice varieties to absorb Na suggests that rice production could be conditionally part of bioremediation of salt-affected soils and water bodies.