Soil water-stable aggregate (WSA) stability is one of the most important indicators of soil health, because it influences chemical, biological and other physical properties. At the same time, WSA formation, stabilization and degradation are also some of the most complex processes that occur in the soil, making them difficult to fully understand. In particular, there is a lack of research on WSA stability in the Baltic region. To gain a better understanding how aggregation occurs in Estonian pedo-climatic conditions, this study was conducted in 2014-2015 in a sandy loam Stagnic Luvisol (LV-st) (WRB, 2014). Potato and barley plots were analysed in a three-year crop rotation (potato → spring wheat → barley) with straw removal. The nitrogen (N) fertilization treatments were 0, 40, 80, 120 and 160 kg ha-1 yr-1 N, both without and with 40 Mg ha-1 fermented cattle farmyard manure (FYM) application prior to potato planting in the previous autumn. WSA stability was determined by Eijkelkamp's wet sieving apparatus from air-dried soil samples of less than 2 mm in diameter. The study revealed a negative correlation (r = −0.16) between increased N rates and WSA stability, regardless of FYM applications. Although soil organic carbon (SOC) content increased with additional N fertilization rates, the reduction in soil acidity (pH KCl) levels caused by N fertilization, most likely repealed the positive SOC content effect on WSA stability. In general, compared with sole N fertilization, FYM application had a positive effect on WSA stability. However, even though WSA stability did not always increase with FYM applications, it still had a positive effect on bulk density, SOC content and soil acidity levels. Further research is needed in Estonia due to the complexities involved in the soil aggregation process.