Nitrate leaching into groundwater is a serious issue in many parts of the world. Usually agricultural use of fertilizers is blamed to be the main source of pollution, but other human activities, like leaky or inexistent sewage systems can also be important in this regard. The aim of this study is to assess nitrate transport from soil to ground and surface waters with nuclear techniques. Two study sites were chosen—both featuring agricultural production in vulnerable areas of alluvial plains. Shallow groundwater below the surface is the main source of drinking water in both areas. Stable isotope techniques provide an innovative and unique methodology to trace and monitor the movement of nitrates (organic and inorganic) from the soil to ground and surface waters and to determine possible sources.