Agricultural drainage and associated water management systems are designed to eliminate to an acceptable level the factors associated with excess water that limit crop growth. In order to eliminate excess water in cultivated areas, it is important to reduce the leaching of nitrogen compounds flowing together with drainage water, as well as to ensure the safe and sustainable use of plant protection products and fertilizers. One possible solution is to transform free drainage structures into controlled drainage systems. In such systems, it is possible to regulate the groundwater level according to the needs of the plants and reduce the leaching of nutrients with drainage water. This paper presents a comparative analysis of controlled and free drainage water pollution by nitrogen compounds. The research was carried out in Pasvalys district, where both types of drainage systems operate next to each other.