In paper evaluation of nitrogen balance and loading of agricultural soil by animal manures with respect to potential water pollution is presented. Soil surface nutrient balance was calculated on country level as well as on farm level on set of selected farms in Trnava province for years 1999 and 2000. Obtained results show that N balance is positive as on state level (20.3 and 37.6 kg N per ha, respectively) as well as on farm level, where average values are little higher (23.2 and 44.9 kg N.ha-1, respectively). OECD provisional limit value +50 kg N.ha-1 was exceeded in 31% of cases. Relative share of manageable N sources (animal manures and fertilisers) on total nitrogen input is 67.9% on farm level and 64.2% on state level and creates sufficient space for reducing the risk of potential water resources pollution. Average loading of agricultural soil by nitrogen from animal manures was on selected set of farms higher (35.1 kg N.ha-1) than on state level (23 kg N.ha-1) but still deep under the Nitrate directive limit. Nitrogen excess or deficit in short period as well as loading of agricultural soil by nitrogen from animal manures can serve as indicators of potential pollution of water resources. From view-point of objective and precise evaluation of data in relation to water sources pollution by nitrogen from agriculture it is necessary to consider as soil parameters as well as manure management quality. This evaluation should be based on farm and sub-farm level even when agricultural subjects do not use the agricultural soil equally intensively.