Purpose <p>Short- and long-term effects of a varying annual rate of nitrogen (N) inputs on plant N uptake and N balance at a constant mean level of fertilization are seldom studied. Applied N may or may not be utilized by crops. This leads to a positive, neutral or negative balance between inputs and outputs. Although the balance could not be exactly determined, it should subsequently change measurable pools or fluxes of N in soil during long-term field investigation.</p> Methods <p>Influence of varying annual N fertilization rates on soil N pools (soil mineral nitrogen), N fluxes (outputs through plant N uptake and leaching) and balance between inputs and outputs, was studied in a 21-year field lysimetric experiment. We hypothesized that each N input into the soil or loss from the soil changes remaining pools and fluxes of N. We also hypothesized that a long-term deficit decreases, and a surplus increases, soil mineral nitrogen (N_min), plant N uptake and losses. </p> Results <p>At given N input rate, the mean annual crop N uptake was higher than the inputs at 7 of 8 locations. An increasing rate of annual N input increased crop N uptake, with only a marginal effect on N_min concentration and leaching.</p> Conclusions <p>Results show, that internal soil resources provided up to 100&#xa0;kg N to annual N uptake and from 100&#xa0;kg N ha^− 1 of annual N input, 40–50&#xa0;kg N is harvested and the rest of added N is retained in soil and released later, independently on actual rate of input. Despite a negative N balance, long-term changes were limited. The results suggest that non-estimated sources of N help to maintain sustainability of the studied cropping systems.</p>