The natural radioactivity of 238U, 232Th and 40K was measured in water and sediment samples collected from Sidi Salem dam (Tunisia) and Aïn Dalia dam (Algeria) in the Tuniso-Algerian transboundary basin. The samples were measured using a TERRA detector of gamma, beta, and alpha rays, and atomic absorption and gamma-ray spectrometry were used to analyze the levels of radionuclides and toxic elements, respectively. Potentially toxic elements (Fe, Pb, Zn, Ni, Cr, Cu and Cd) and associated health risks in surface water and sediment of dams were investigated in this present study. The concentrations of Fe, Pb, Zn, Ni, Cr, Cu and Cd in surface water ranged from 5.430 to 9.700 mg·L−1, 0.022 to 0.168, 0.018 to 0.142, 0.065 to 0.366, BDL to 0.0351, BDL to 0.071 and BDL to 0.048 mg·L−1, respectively. In the sediments, the concentrations of Fe, Pb, Zn, Cu, Ni, Cd and Cr were of the order of 136.7, 3.41, 3.22, 0.213, 0.182, 0.15 mg·L−1 and BDL, respectively. The mean radioactivity rates in the water samples were 1.72, 0.068 and 94.6 Bq·L−1 for 238U, 232Th and 40K, respectively (Tunisia dam), and were 1.9, 0.09 and 131.43 Bq·L−1 for 238U, 232Th and 40K, respectively (Algeria dam). The mean 238U, 232Th and 40K radioactivity concentrations measured in the sediment samples were 2.67, 0.18 and 197.87 Bq·kg−1, respectively (Tunisian dam), and were 4.34, 0.27 and 287.61 Bq·kg−1, respectively (Algeria dam). The activity concentration of 40K was higher than that of 238U and 232Th for the water and sediment samples. The activity concentrations follow the order 40K > 238U > 232Th. The cumulative impact of these radio-geochemical elements can cause immediate serious problems in the ecosystem due to their high potential toxicity to the environment and human health in this study area and can be transposable to any other similar region. A good knowledge of monitoring quality and quantity for transboundary water resources and international collaborations are essential to safeguard human health (women’s breast cancer, thyroid cancer, neurological impact) and avoid conflicts, especially during climatic upheavals of drought.