Growing cities in densely populated delta areas around the globe require year-round access to sufficient fresh water and protection against flood events from the river or sea. Therefore, water storage and flood protection is regulated by dams and dykes, resulting in the creation of artificial lakes in these deltas. Besides the main purposes for which these lakes were constructed, they also provide a wide range of other ecosystem services like for example recreation or food production. Moreover, these lakes can be considered to be important wetland habitats, characterized by shallow fresh waters with soft sediments, with a high potential for ecological developments. However, in reality the water levels and shorelines are predominantly artificial, and the water quality is often poor due to pollution and changed hydrology. This is also the case in lake Markermeer, a large and shallow reservoir created in the Rhine delta in the central part of the Netherlands. After closure of the last dyke in 1975, the lake became strongly influenced by habitat modifications, resuspension of fine sediments and changed nutrient dynamics. This has resulted in an ecological collapse during the past decades. Here, we will present results of experiments and field monitoring, studying the influence of biotic and a-biotic benthic processes on productivity and food-web structure in lake Marken. By analyzing the main drivers underlying the observed changes in relation to the negative impacts, essential insight is generated to effectively restore the ecological functioning of ecologically impaired constructed delta lakes.