Soil erosion is a widespread phenomenon threatening the sustainability of agricultural production in the South-Kivu highlands (eastern D.R. Congo), as is the case in other cultivated areas of the East-African highlands. However, quantitative estimates of soil erosion on farm are scarce. To address this, the extent of erosion and associated explanatory factors were studied in two representative watersheds across a wide range of cropping systems and soil characteristics. Rill and gully erosion volumes were measured every 2 weeks in 90 fields by the transect methods during four successive long (SA) and short (SB) rainy seasons (2015–2017). Additionally, field characteristics and rainfall were collected. Results show that the average soil loss rate was significantly different between seasons, with rates of 3.1 and 1.9 mm in season A-2015, 1.8 and 2.7 mm in season B-2016, 2.2 and 3.3 mm in season A-2016 and 3.2 and 3.8 mm in Season B-2017 for minimum rill (damage area) and gully erosion (whole field), respectively. As a result of differences both in natural factors (e.g., precipitation and slope steepness) and management conditions (cropping systems and soil cover) across farmers' fields, there was a large variability in cumulative soil erosion rates across fields, from 0.03 to 18 mm for minimum rill erosion and from 0.13 to 11.7 mm for gully erosion rates over the 4 seasons. For 41% of fields, rill erosion rates are higher than the tolerable soil loss generally set at 12.5 t/ha/year (or 1 mm/year) for the most fertile soils. Low minimum rill erosion rates tended to be associated with high pH, sum of bases and effective CEC, while high erosion rates were associated with high topsoil depth in both watersheds. Cassava-based cropping systems tended to be associated with high rill erosion rates, while higher rainfall increased both rill and gully erosion rates. Overall, the very high measured rill erosion rates suggest the urgent need for implementation of erosion control strategies. The results could be used to prioritize sites at risk of water erosion at the small watershed scale in order to install mitigation measures.