Plant seeds are highly sensitive to environmental stress. The aim of our paper was to assess the effects of high nutrient levels in the water and sediment of thermal ponds and rivers on the ecosystem, based on the seed germination and root elongation of S. alba in the Lëngaricës Valley, Albania. Significant differences were found in the physicochemical parameters of the water and the sediment among samples taken from the river, the thermal ponds, and the control ponds. We found significant differences in the root elongation of S. alba seeds based on the water and the sediment of the river, the thermal ponds, and the control ponds. Significantly longer roots were found in the thermal water and sediment than in the river. Among the physicochemical parameters of the water and the sediment, Cu, K, and Li were stimulants for root elongation. With Cu, Li, Ba, Mg, Ni, carbon-dioxide, and sulphate-ion, a stimulant effect was found on seed germination. Our results indicated that the high mineral level of the water and sediment of these thermal ponds had positive effects on the ecosystem based on seed germination and the root elongation test of S. alba.