Seagrass ecosystems have experienced a dramatic decrease in recent years and high water column nutrients as well as changes in grazer diversity are regarded as major drivers of this decline. Few studies have assessed the relative importance of top-down grazer effects in combination with bottom-up nutrient effects on the entire seagrass community. In this study we used indoor mesocosms with constantly high nutrient supply and manipulated grazer diversity. We considered the seagrass habitat as a whole by including the seagrass-epiphyte community and the microphytobenthos beneath a Zostera marina bed. Nutrients significantly affected the composition and diversity of microalgal communities and on the long run eutrophication clearly took on a governing role. Grazer diversity influenced the microalgal communities on the short-term. During the course of the experiment the high food quantities boosted the grazers biomass and reproduction. However, the consumers were unable to control the strong microalgal production. This experiment provides evidence that constantly high nutrient loadings can affect seagrass communities considerably and that grazers at intermediate abundance are unable to sustain the stability at high levels of primary productivity.