Nitrates represent one of the main groups of contaminants in the Zagreb aquifer system. Some natural groundwater quality indicators can have a significant influence on their stability and mobility in the saturated zone. Correlation and multivariate statistical analyses were used to test the correlation of average values of NO3- with O2, ORP, pH, EC and temperature of groundwater, and to allocate observation wells that belong to the same clusters. ORP values didn't relate to any observed variables, which is probably due to their variability which suggests changes in the oxidation-reduction conditions in the aquifer system. Principal component analysis was used for the determination of variables that are related to the nitrate concentrations and which were then used in cluster analysis. Other variables were excluded from cluster analysis. Three methods were used to perform cluster analysis, where the results calculated with Ward's method were chosen as the most appropriate. In the end, two clusters were identified, one with smaller, and one with higher NO3-, O2 and EC values. Observation wells from cluster 1 are generally located near the Sava River and have similar nitrate concentrations. Lack of other nitrogen species and moderately aerobic conditions suggest very fast nitrification in the shallow Holocene aquifer.