Although invasive species often resemble their native counterparts, differences in their foraging and anti-predator strategies may disrupt native food webs. In a California estuary, we showed that regions dominated by native crabs and native whelks have low mortality of native oysters (the basal prey), while regions dominated by invasive crabs and invasive whelks have high oyster mortality and are consequently losing a biologically diverse habitat. Using field experiments, we demonstrated that the invasive whelk’s distribution is causally related to a large-scale pattern of oyster mortality. To determine whether predator–prey interactions between crabs (top predators) and whelks (intermediate consumers) indirectly control the pattern of oyster mortality, we manipulated the presence and invasion status of the intermediate and top trophic levels in laboratory mesocosms. Our results show that native crabs indirectly maintain a portion of the estuary’s oyster habitat by both consuming native whelks (density-mediated trophic cascade) and altering their foraging behavior (trait-mediated trophic cascade). In contrast, invasive whelks are naive to crab predators and fail to avoid them, thereby inhibiting trait-mediated cascades and their invasion into areas with native crabs. Similarly, when native crabs are replaced with invasive crabs, the naive foraging strategy and smaller size of invasive crabs prevents them from efficiently consuming adult whelks, thereby inhibiting strong density-mediated cascades. Thus, while trophic cascades allow native crabs, whelks, and oysters to locally co-exist, the replacement of native crabs and whelks by functionally similar invasive species results in severe depletion of native oysters. As coastal systems become increasingly invaded, the mismatch of evolutionarily based strategies among predators and prey may lead to further losses of critical habitat that support marine biodiversity and ecosystem function.