In the last decades, zebra mussels (Dreissena polymorpha) have invaded many freshwater systems with severe consequences for entire communities. Most benthic macroinvertebrates, especially amphipods and chironomids, increase in abundance in the presence of zebra mussels. Increased structural complexity and an unknown biotic factor lead to this effect. Dreissena-associated factors that might influence populations of the native Gammarus roeselii and the invader Dikerogammarus villosus in Lake Constance, Central Europe, were investigated in laboratory experiments. These factors were: 1) increased structural complexity related to mussel shells, 2) Dreissena biodeposition, 3) chironomids, the presence of which is increased by biodeposited matter, and 4) Dreissena kairomones. In habitat-choice experiments, the native and omnivorous amphipod G. roeselii showed a preference for mussel shells with biodeposited material and for mussel shells with biodeposited material with chironomids, whereas the invasive and predatory amphipod D. villosus showed a preference only for mussel shells with biodeposited material with chironomids. In a kairomone y-maze experiment, both amphipods avoided zebra-mussel-conditioned lake water. These results indicate that habitat complexity and food availability, mediated directly or indirectly through biodeposited material, are the factors by which amphipod abundances are increased in the presence of Dreissena. Thus, biodeposited material can form an important new food resource, translocated from the pelagic zone to the benthos by zebra mussel filtration, and this biodeposited material might support a new detritus-based food web in the benthos.