Land-water transition areas play an important role in the functioning of both aquatic and terrestrial ecosystems. Enhancing habitat complexity and heterogeneity by restoring or adding land–water transition areas to degraded aquatic ecosystems can be effective management to stimulate productivity by lower trophic levels – and hence increase food availability for biota of conservation interest, including fish and birds. Here, we studied whether hydrological connectivity can be used as an environmental indicator (connected or disconnected) for the development trajectories of newly constructed land–water transition areas in shallow lakes. We capitalized on a large-scale restoration project called “Marker Wadden”, which created new land–water transition areas with and without hydrological connectivity in a degraded shallow lake in the Netherlands (Lake Markermeer). We compared how the new areas with and without hydrological connectivity developed with respect to abiotic parameters and biomasses of benthic, pelagic, and emergent macroinvertebrates. In sites disconnected from the open water, water depths became significantly lower than in hydrologically connected sites during summer, likely due to evaporation. In these shallower waters, daytime temperatures and organic matter content of the sediment were higher, while dissolved oxygen concentrations remained sufficient. Therefore, biomasses of benthic macroinvertebrates and emergent insects became higher in the disconnected sites. These lower trophic levels could provide higher food availability for benthivorous and insectivorous birds, while remaining inaccessible to fish. This puts forward that hydrological connectivity (connected or disconnected) can be used as an environmental indicator for aquatic food web development trajectories, and that it regulates relative food availability for fish and birds. Restoring land–water transition areas without hydrological connectivity provides higher biomasses of lower trophic levels, which are only accessible to birds. Restoring areas with hydrological connectivity results in relatively lower biomasses of invertebrates, but these provide food to birds feeding on invertebrates, and fish and fish-eating birds. Creating areas including both types of land–water transition zones, connected and disconnected to open water can benefit fish and birds of both feeding guilds.