In order to study the soil aggregate distributions and soil organic matter (SOM), we sampled top- and subsoils in four intensively farmed croplands (two organic (Org-OB and Org-LA), and two conventional (Con-OB and Con-LA)) on Haplic Chernozems located in Marchfeld in the east of Vienna (Austria). Soil structure and SOM quantity, quality and distribution between free and occluded particulate organic matter and aggregate size fractions (<20 µm, 20-250 µm, 250-5000 µm) were studied by following a density fractionation procedure with low-energy ultrasound treatment. The relation of the soil physicochemical (e.g., particle size distribution, pH, organic carbon, total nitrogen) and biological properties (e.g., fungal biomass, active fungi) with stable soil aggregate size fractions and SOM was studied. The mean weight diameter (MWD) showed no significant difference between all studied sites and was between 3.8 mm and 10.0 mm in topsoils and between 6.7 mm and 11.9 mm in subsoils. In topsoils, the contents of calcium-acetate-lactate (CAL)-extractable P, active fungal biomass, dithionite-extractable Fe and sand were significantly positively correlated with the amount of the macroaggregates and with the MWD. We observed that most soil organic carbon, depending on soil texture, was stored in the microaggregate size classes <20 µm and 20-250 µm.