Soil erosion is one of the eight threats in the Soil Thematic Strategy, the main policy instrument dedicated to soil protection in the European Union (EU). During the last decade, soil erosion indicators have been included in monitoring the performance of the Common Agricultural Policy (CAP) and the progress towards the Sustainable Development Goals (SDGs). This study comes five years after the assessment of soil loss by water erosion in the EU [Environmental science & policy 54, 438–447 (2015)], where a soil erosion modelling baseline for 2010 was developed. Here, we present an update of the EU assessment of soil loss by water erosion for the year 2016. The estimated long-term average erosion rate decreased by 0.4% between 2010 and 2016. This small decrease of soil loss was due to a limited increase of applied soil conservation practices and land cover change observed at the EU level. The modelling results suggest that, currently, ca. 25% of the EU land has erosion rates higher than the recommended sustainable threshold (2 t ha−1 yr−1) and more than 6% of agricultural lands suffer from severe erosion (11 t ha−1 yr−1). The results suggest that a more incisive set of measures of soil conservation is needed to mitigate soil erosion across the EU. However, targeted measures are recommendable at regional and national level as soil erosion trends are diverse between countries which show heterogeneous application of conservation practices.