The main problem in the trans-boundary river system is that heavy metal and radioactive pollution can cause long-term effects on ecosystems. Therefore the natural radioactivity and heavy metal levels in the Maritza, Tundja and Arda Rivers, common for Bulgaria and Turkey, were determined for 3 years period (2007-2010). Gross alpha, gross beta and total radium isotopes activities, uranium and heavy metal concentrations of the surface water of the rivers were investigated and also terrestrial gamma and gamma dose rate were measured. The results were compared with reported data from other countries of the world and the recommended international standards. The results gathered in this study may provide background data on the natural radioactive and heavy metal levels of these trans-boundary rivers.