Current rates of habitat loss require science-based predictions on how to restore or newly create lost habitat types. In aquatic ecosystems, littoral zones are key habitats for food web functioning, but they are often replaced by unnatural steep shorelines for water safety. To reverse this trend, knowledge is needed on how to successfully (re)create littoral zones. We quantified the response of an aquatic food web to the large-scale creation of new heterogeneous littoral habitats in shallow lake Markermeer, the Netherlands. Lake Markermeer was formed by dike construction in a former estuary, which created a heavily modified homogeneous 70,000 ha turbid lake lacking littoral habitat. Fish and bird populations declined over the last decades, but classical restoration via return to former marine conditions would compromise water safety and the large spatial scale prohibited biodiversity offsets. Therefore, an innovative “forward-looking restoration” approach was adopted: a 1000 ha archipelago called “Marker Wadden” was constructed without using a historic reference situation to return to. This aimed bottom-up stimulation of the aquatic food web by added missing gradual land-water transitions and sheltered waters to the lake. After four years, new sheltered shorelines had become vegetated if they were constructed from nutrient-rich sediments. Exposed and sandy shorelines remained free of vegetation. Zooplankton community diversity increased in sheltered waters due to bottom-up processes, which increased food availability for higher trophic levels, including young fish. The creation of sheltered waters increased macroinvertebrate densities threefold, with sediment type determining the community composition. The archipelago became new nursery habitat for 13 of the 24 fish species known to occur in the lake, with up to 10-fold higher abundances under sheltered conditions. We conclude that modifying abiotic conditions can stimulate multiple trophic levels in aquatic food webs simultaneously, even in heavily modified ecosystems. This provides proof-of-principle for the forward-looking restoration approach.