Many studies on invasive species show reduced native densities, but few studies measure trait-mediated effects as mechanisms for changes in native growth rates and population dynamics. Where native prey face invasive predators, mechanisms for phenotypic change include selective predation, or induced behavioral or morphological plasticity. Invasive green crabs, Carcinus maenas, have contributed to declines in native soft-shell clams, Mya arenaria, in coastal New England, USA. We tested the hypothesis that clam ability to detect chemical cues from predators or damaged conspecifics would induce greater burrowing depth as a refuge from invasive crabs, and greater burrowing would require increased siphon growth. To determine how crab predation affected clam survivorship and phenotypic traits in the field, clams in exclosure, open, and crab enclosure plots were compared. Crab predation reduced clam density, and surviving clams were deeper and larger, with longer siphons. To determine whether the mechanism for these results was selective predation or induced plasticity, phenotypes were compared between clams exposed to chemical cues from crab predation and clams exposed to seawater in laboratory and field experiments. In response to crab predation cues, clams burrowed deeper, with longer siphons and greater siphon mass. Overall, crab predation removed clams with shorter siphons at shallow depths, and crab predation cues induced greater burrowing depths and longer siphons. Longer siphons and greater siphon mass of deeper clams suggests clams may allocate energy to siphon growth in response to crabs. By determining native behavior and morphological changes in response to an invasive predator, this study adds to our understanding of mechanisms for invasive impacts and illustrates the utility of measuring trait-mediated effects to investigate predator–prey dynamics.