Macrophytes and nutrient loading are two factors that can strongly determine the diversity and composition of aquatic invertebrate communities. Both factors may also interact, because macrophyte species may be differentially affected by nutrients. Macrophyte community characteristics, such as species composition, morphotype and biomass have the potential to mediate the response of invertebrate communities to nutrient loading. In 36 newly constructed experimental ponds,weorthogonally combined three macrophyte community types (Chara-, Potamogeton- and Elodea-dominated) with two levels of nutrient additions (no addition and an addition of 0.5 mg P and 3mg N/L per week) and studied community assembly in three functional groups of invertebrates (epiphytic macroinvertebrates, littoral and pelagic crustacean zooplankton). Macrophyte biomass was negatively affected by nutrient addition. General linear models indicated negative responses of species richness in the zooplankton functional groups to nutrient addition and phytoplankton chlorophyll-a, but demonstrated no effects of macrophyte community type. Conversely, macroinvertebrate taxon richness differed among macrophyte community types but showed no response to nutrient enrichment. Macrophyte biomass correlated positively with the richness of littoral zooplankton and macroinvertebrates and was a better predictor of these diversity variables than macrophyte community type. Overall, our results indicate that lake management practices that aim at obtaining a nutrient poor and macrophyte dominated clear water state contribute also to the maintenance of aquatic invertebrate diversity.