Species loss can result in secondary extinctions and changes in ecosystem functions at distant trophic levels. Such effects of species loss are predicted to be affected by both the number of species lost within a trophic level (horizontal diversity) and the number of trophic levels lost (vertical diversity). We experimentally manipulated horizontal and vertical diversity within an aquatic insect community, and examined responses throughout the food web. Horizontal and vertical diversity both impacted ciliates: reduction of detritivorous insect diversity resulted in secondary extinctions and decreased density of ciliates, but only when an insect predator was simultaneously absent. Horizontal and vertical diversity differed in their effect on other foodweb processes, including detrital processing, predator growth, and densities of rotifers, flagellates and flatworms. These results caution that foodweb effects of multitrophic species loss may not be reliably predicted from manipulations of just one dimension of diversity.