The gramineous species Andropogon lateralis and Paspalum notatum dominate lowland habitats in Paraguay. These habitats include wetlands and aquifers that provide essential ecosystem services, such as soil C storage, biodiversity, water flow regulation and water quality. Large areas of these valuable natural ecosystems have been transformed into intensive agricultural systems, including sugarcane and eucalyptus plantations. The transformation potentially affects water flow and lake and stream recharge and threatens the native biodiversity of the ecoregion. The soils in these zones are characterised by high C stocks, high acidity, nutrient limitation (low cation exchange capacity and base saturation) and a sandy texture, and they may be sensitive to perturbations. This study aimed to assess the impact of eucalyptus plantations on soil properties and nutrient and C stocks in afforested lowland regions in a subtropical area and to generate information relevant to sustainable management. For this purpose, 62 eucalyptus plantations of ages between 2 and 10 years and 8 native grassland plots were selected for study. The experimental design enabled us to estimate the amounts of nutrients extracted throughout the plantation rotation and to evaluate the impacts on soil properties (at 0–40 cm depth) and on soil carbon and nutrient stocks. The eucalyptus biomass production amounted to 215 Mg ha−1 after 10 years. The significant loss of soil C, which had decreased to 40 % after a decade, was attributed to the initial soil preparation, intensive drainage and the lower input of organic remains than in the natural grasslands. The significant decreases in soil nutrient stocks (N, P, Ca, Mg, and K), reaching between 50 % and 60 % throughout the rotation, were attributed to uptake of these elements by the trees. The bulk density increased by up to 1.3 g cm−3. The data suggest that establishing eucalyptus plantations in these lowland habitats leads to soil degradation and may reduce the environmental services supplied by the ecosystems. Local authorities must develop and implement territorial land plans and silvicultural practices in order to prevent degradation of these critical ecosystems. • Biomass production is typically high in the study plantations (21.5 Mg ha−1 year−1). • Nutrient and C stocks decrease after afforestation with eucalyptus trees. • Harvesting leaves and bark leads to export of large amounts of N, Ca, Mg and P. • The eucalyptus plantations increase the soil acidity in the study system. • Sustainable forest management and soil conservation practices must be implemented. [ABSTRACT FROM AUTHOR]