AbstractThe capacity of an apex predator to produce nonconsumptive effects (NCEs) in multiple prey trophic levels can create considerable complexity in nonconsumptive cascading interactions, but these effects are poorly studied. We examined such effects in a model food web where the apex predator (blue crabs) releases chemical cues in urine that affect both the intermediate consumer (mud crabs seek shelter) and the basal prey (oysters are induced to grow stronger shells). Shelter availability and predator presence were manipulated in a laboratory experiment to identify patterns in species interactions. Then, experimentally induced and uninduced oysters were planted across high‐quality and low‐quality habitats with varying levels of shelter availability and habitat heterogeneity to determine the consistency of these patterns in the field. Oyster shell thickening in response to blue crab chemical cues generally protected oysters from mud crab predation in both the laboratory and in field environments that differed in predation intensity, structural complexity, habitat heterogeneity, and predator composition. However, NCEs on the intermediate predator (greater use of refugia) opposed the NCEs on oyster prey in the interior of oyster reefs while still providing survival advantages to basal prey on reef edges and bare substrates. Thus, the combined effects of changing movement patterns of intermediate predators and morphological defenses of basal prey create complex, but predictable, patterns of NCEs across landscapes and ecotones that vary in structural complexity. Generalist predators that feed on multiple trophic levels are ubiquitous, and their potential effects on NCEs propagating simultaneously to different trophic levels must be quantified to understand the role of NCEs in food webs.