Central in the policies for lake Markermeer, including the EU Water Framework Directive and N2000, is the pursuit of a robust and resilient nature in synergy with other uses. Recently, various measures have been taken to fulfill these policy goals. The question arises wheth-er these measures will provide successes. Therefore, we studied the benthos that plays a key role in lake func-tioning and determines 55-75% of the food relationships for the recently strongly declined fish and bird species. A decline may be due to the poorly developed benthos. Worms currently dominate lake Markermeer, at a dis-tance followed by quagga mussels. Compared to natu-ral reference lakes, macroinvertebrate numbers are low (meaning a low food availability), and bioturbation and bio-irrigation levels are limited. The poorly developed benthos indicates that the current stock of particular organic material is insufficient. Therefore, the ben-thos is hindered to connect lakebed and the water col-umn. Strengthening the natural flux of organic mate-rial and nutrients is the missing link in restoring lake Markermeer functioning. By connecting impounded and new marshlands as well as by creating shallow litto-ral zones, organic material cycling will be initiated and enforced, and landscape, biotope and habitat heteroge-neity will be strongly improved.