Biomanipulation through fish removal is a tool commonly used to restore a clear-water state in lakes. Biomanipulation of ponds is, however, less well documented, although their importance for biodiversity conservation and public amenities is undisputed. In ponds, a more complete fish removal can be carried out as compared to lakes and therefore a stronger response is expected. Fish recolonization can, however, potentially compromise the longer term success of biomanipulation. Therefore, we investigated the impact of fish recolonization on zooplankton, phytoplankton, and nutrients for several years after complete drawdown and fish removal in function of submerged vegetation cover in 12 peri-urban eutrophic ponds situated in Brussels (Belgium). Fish recolonization after biomanipulation had a considerable impact on zooplankton grazers, reducing their size and density substantially, independent of the extent of submerged vegetation cover. Only ponds with \30% cover of submerged vegetation shifted back to a turbid state after fish recolonization, coinciding with an increase in density of small cladocerans, rotifers, and cyclopoid copepods. In ponds with [30% submerged vegetation cover, macrophytes prevented an increase in phytoplankton growth despite the disappearance of large zooplankton grazers. Our results suggest that macrophytes, rather than by providing a refuge for zooplankton grazers, control phytoplankton through other associated mechanisms and confirm that the recovery of submerged macrophytes is essential for biomanipulation success. Although the longer term effect of biomanipulation is disputable, increased ecological quality could be maintained for several years, which is particularly interesting in an urban area where nutrient loading reduction is often not feasible.