The Neretva valley, a total area of 12 067 ha represents a specific natural geographical space cut into karst area. The southern border of the area is the Adriatic Sea. The population, agriculture, and the entire living world are adapted to the water regime of the natural environment. The most significant pressure on the area of the Neretva valley, which can adversely affect the sustainability of agricultural land and the whole ecosystem is soil salinization, which is associated with the degree of salinity of surface and groundwater. The immediate vicinity of the sea, expressed the seawater in the valley, even temporarily or permanently salinated water sources used for irrigation. Primary endangered soil of constantly performs fertilization, always the same schedule, depending on the crop is grown. When it comes to leaching of nitrates in surface water and groundwater under the influence of rainfall. For these reasons there is a need to establish control over further processes salinization of water and soil of the Neretva valley, and adherence to the principles of good agricultural practices, in order to exploit the full potential for good agricultural production, but also to protect natural resources. The survey includes significant locations by intensive cultivation of crops, and in which we examined the relationship between nitrate and total precipitation in salt and water resources. The results showed the location with the highest concentration of nitrates (Pz-2 installed in the field Vidrice) and salt (Pz-2 installed in the field Opuzen ušće- Jasenska), and it was found that an increase in rainfall leads to leaching of nitrates in surface and ground waters. Decreasing rainfall comes to increase the EC in surface waters, and groundwater, this rule does not apply. In order to reduce the concentration of nitrate and total salts in the water resources of the Neretva valley, it is recommended to comply with the provisions of the Nitrates Directive, as well as the use unsalted water sources for irrigation in agriculture.