In the last few years, environmental pollution has been major concern in Croatia. In some parts of Croatia, uncontrolled and extensive production is causing the pollution of groundwater with nitrates, nitrate, ammonium, oils, phenols etc. An example of area with groundwater quality problems is the surrounding area of the town Varaždin. The area is densely populated and industrial and agricultural production are well developed. Because of high concentrations of nitrates, ammonium, oils and phenols, one pumping site is shut down. Since problems relating to high nitrate concentrations occurred in the research area, intensive research of source, distribution and fate of nitrogen and carbon have been carried on. Carbon has been studied because it is present in molecules that are integral to all living creatures, as carbon dioxide and methane in the atmosphere, in carbonate rocks in the lithosphere and as organic molecules in soils and sediments that are derived from formerly living material and it can be used to determine the source of the pollution. For the research purposes, a monitoring network has been established. Water samples have been taken from 10 observation wells and 4 surface water locations (river, stream, gravel pit and lake) on monthly basis. Prior to sampling, electrical conductivity, pH, temperature and dissolved oxygen content are determined by using portable WTW probes. Groundwater and surface water samples are being collected for various analyses: major cations and anions, REE, stable isotopes D, 18O and 13C , stable isotopes 18O and 15N in nitrate and nutrients (nitrate, nitrite, ammonia, phosphate, TN, TOC, DOC and TIC). In addition, soil sampling under various vegetation cycle and from different land use plots were collected. Soil’s mineralogy, especially clay minerals, chemical properties and nutrients content (organic and inorganic carbon and total nitrogen) were measured. Preliminary results showed that concentrations of TOC are almost equal to DOC concentrations in ground and surface waters. The higher concentrations of TOC and DOC are observed in surface water than in groundwater. The highest values are measured in the water of the gravel pit. According 13C ratio, gravel pit and lake waters are distinguished from ground and stream/river waters. Soil samples in the orchards contains the highest concentration of the organic carbon wail the lowest are measured in soil samples taken from cornfield.