Integrated monitoring of the effects of aggregate extraction is needed to reach Good Environmental Status of the marine environment by 2020 (European Marine Strategy Framework Directive (MSFD); 2008/56/EC). This requires increased process and system knowledge that incorporates both natural and human-induced variability. Additionally, when exploitation is within or near Habitat Directive Areas, appropriate assessments are needed of all stressors (92/43/EEC). Recently, new extraction activities started in a far offshore sandbank area in the Belgian part of the North Sea, just north of a Habitat Directive Area. Therefore, a dedicated monitoring programme was set-up, with focus on assessing changes in seafloor integrity and hydrographic conditions, two descriptors that define Good Environmental Status.Since extraction started in 2012, monitoring results are short-term and relate to: (1) natural variability; (2) sediment plume formation and deposition, differentiating between small and large trailing suction hopper dredgers; (3) far–field impacts, with focus on the nearby Habitat Directive Area, where ecologically valuable gravel beds occur. New insights were revealed on the three levels, though most striking was enrichment of fines in the coarse permeable sands of the gravel area. No direct relationship could yet be made between the intensive extractions and the mud enrichment, though MSFD requires further monitoring of the gravel beds, since favourable colonization and growth of epifauna is critical for the maintenance and increase of biodiversity in the Belgian part of the North Sea.