Over the past fifty years, the public has recognized the need to protect quality and quantity of groundwater from karst aquifers as a source of potable water in Croatia and the world. Due to their specific characteristics, such as a thin soil cover, concentrated infiltration, swallow holes and concentration of flow in the epikarst and vadose zones, karst aquifers are known for their sensitivity to pollution. Contaminants can be transported very fast or even stored depending on the existence of fast or slow flow components in a karst system. Due to its reactivity, soil and sediment represent a significant factor in retardation and attenuation of potential pollution on its way to groundwater. Dugopolje is a typical karst field located on the northern slopes of the Mosor mountain facing northwest-southeast and sloping slightly toward the southeast. The area consists largely of mesozoic and kenozoic carbonate and clastic rocks. Because of the intensive tectonics, area is intensively karstified with couple of active swallow holes. The soils comprise brown and red soils on limestones and dolomites. The new economic zone and the development of road infrastructure (mainly Adriatic highway) have so far transformed the rural landscape into one of the most propulsive areas in Croatia, and the number of people who have found work there exceeded the number of permanent residents of the area. Along with the economic progress, came the danger of soil and groundwater contamination that is noticeable in deterioration of water quality of Jadro and Žrnovnica springs. The intrinsic vulnerability takes into account the geological, hydrological and hydrogeological properties of the area, regardless of the contaminant properties and the means of contamination, whereas specific vulnerability takes into account the properties of each individual contaminant. In this paper, the intrinsic vulnerability was assesed using the COP method to determine the most vulnerable areas that need special protection. Based on the map of the intrinsic vulnerability, a map of specific vulnerability has been developed. It takes into account the physical and geochemical properties of the soil, the unsaturated and saturated zones and processes associated with them, the properties of a particular type of contaminant and their behavior under certain geochemical conditions in different parts of the karst aquifers. The behavior of certain types of contamination in the karst aquifers was evaluated based on the results of the analysis and measurement of physical, physiochemical and chemical parameters of karst soil and filling of the epikarst zone. Adjustment of weights factors used in modeling the specific vulnerability of groundwater was performed according to geochemical conditions in various parts of the karstic hydrogeological system covered in red soil. The results of geochemical modeling using PHREEQC directly indicate the ionic form or the method of transport of chosen contaminant species. Arsenic and lead are predominantly related to the suspended soil and sediment particles and nitrates are migrable in the form of ions. Therefore, the mentioned contaminants can be transported over long distances without significant change. The obtained results have contributed significantly to the understanding of the soil and the epikarst zone storage capacity, not only in the Dinarides, but also in the areas with similar lithological and hydrogeological features. Steps have been taken in the last ten years to ensure improvements in quality of the spring waters of Jadra and Žrnovnica. A series of collectors and laggons were constructed along the Adriatic highway along with the closed water drainage system and sewage network in the Dugopolje area.