Wind-induced sediment resuspension in shallow lakes may enhance nutrient availability while reducing light availability for phytoplankton growth, thereby affecting the entire food-web. Lake restoration projects that reduce wind-induced resuspension are expected to enhance trophic transfer efficiencies, thereby improving food-web structure and functioning. Yet, reduced resuspension may also lead to lower nutrient concentrations in the water column, promote benthic algae development, reduce phytoplankton biomass production and thereby reduce secondary production by zooplankton. Lake Markermeer is a shallow delta lake in The Netherlands subject to wind-induced sediment resuspension. Restoration project Marker Wadden consists of newly built islands aiming to reduce sediment resuspension and promote higher trophic levels. Here, we tested the effects of reduced sediment resuspension on phytoplankton biomass build-up, benthic algae development, and zooplankton abundances at different temperatures in a 14-day indoor microcosm experiment. We used Marker Wadden sediment with three resuspension intensities combined with three temperatures, to also test effects of higher temperatures in shallow sheltered waters. Reduced sediment resuspension decreased nutrient concentrations and phytoplankton biomass build-up, while increasing light availability and enhancing benthic algae biomass development. Reduced sediment resuspension furthermore increased zooplankton biomass. Enhanced sediment resuspension and higher temperatures synergistically interacted, maintaining a high level of inorganic suspended solids. Our experimental results are in line with long-term seasonal observations from Lake Markermeer. Our findings demonstrate that for shallow lakes suffering from wind effects, measures such as Marker Wadden aimed at reducing sediment resuspension can be effective in restoring secondary production and supporting higher trophic levels.