This study aimed to measure the concentrations of carbon (C), nitrogen (N) and the natural abundance of 13C and 15N in macro and microaggregates under systems of land use. We sampled the 0-5 and 5-10 cm layers in no-tillage system (NTS), conventional tillage system (CTS), secondary forest and pasture in southern Brazil. The largest variations of C and N concentrations were found for the 8-2 mm aggregate class, with the sequence pasture > forest = NTS > CTS, compared to the 0.25-0.105 mm class. The most negative δ13C values were found in the microaggregates and the least negative were found in the macroaggregates. Plowing and harrowing in the CTS cause the fracturing of soil aggregates, accelerating the mineralization reactions of soil organic matter (SOM) and discouraging the occlusion of SOM in the aggregates, resulting in higher δ15N values compared to the other systems evaluated. The larger variation in C and N content for the 8-2 mm class and smaller variation in the 0.25-0.150 mm class indicate that there is higher and lower sensitivity to the management system adopted in these areas and lesser and greater protection of the C and N by these aggregate classes, respectively.