The demand for marine sand in the Netherlands as well as globally is increasing. Over the last decades, only shallow sand extraction of 2 m below the seabed was allowed on the Dutch Continental Shelf (DCS). To guarantee sufficient supply and to decrease the surface area of direct impact, the Dutch authorities started to promote sand extraction depths over 2 m for sand volumes over 10 million m3. The ecological effects of deep sand extraction, however, are still largely unknown. Therefore, we investigated short-term effects (0–2.5 y) of deep sand extraction (20–24 m) and compared these with other case studies such as, regular shallow sand extraction on the DCS (2 m) and an 8 m deepened shipping lane. For intercomparison between case studies we used tide-averaged bed shear stress as a generic proxy for environmental and related ecological effects. Bed shear stress can be estimated with a two-dimensional quadratic friction law and showed a decrease from 0.50 to 0.04 N m−2 in a borrow pit in 20 m deep water and extraction depths up to 24 m. Macrozoobenthos in a borrow pit with a tide-averaged bed shear stress of around 0.41 N m–2 is expected to return back to pre-extraction conditions within 4–6 year. When tide-averaged bed shear stress decreases below 0.17 N m−2 enhanced macrozoobenthic species richness and biomass can occur. Below a tide-averaged bed shear stress of 0.08 N m−2, increasing abundance and biomass of brittle stars, white furrow shell (Abra alba) and plaice (platessa platessa) can be expected. Below 0.04 N m−2, an overdominance and high biomass of brittle stars can be expected whereas demersal fish biomass and species composition may return to reference conditions. Next to changes in faunal composition, a high sedimentation rate can be expected. Ecological data and bed shear stress values were transformed into ecosystem-based design (EBD) rules. At higher flow velocities and larger water depths, larger extraction depths can be applied to achieve desired tide-averaged bed shear stresses for related ecological effects. The EBD rules can be used in the early-design phases of future borrow pits in order to simultaneously maximise sand yields and decrease the surface area of direct impact. The EBD rules and ecological landscaping can also help in implementing the European Union's Marine Strategy Framework Directive (MSFD) guidelines and moving to or maintaining Good Environmental Status (GES).