Many taxa possess a range of strategies to reduce the risk of predation, including actively seeking suitable refuge habitats; however, the global spread of invasive species may disrupt these behavioral responses. In lotic ecosystems, interstitial spaces in the substrate are important refugia for small organisms. Some predators are ecosystem engineers that exhibit zoogeomorphic agency-the ability to modify the geomorphology of their environment. It is therefore possible that direct ecological effects of predators on prey may be realized through modifications to the prey's habitat, including the availability of refugia, by predators that are zoogeomorphic agents or via external stressors such as fine sediment loading. This study examined three research questions in a mesocosm study across a gradient of sediment-stress treatments: (1) What affects do predators (Pacifastacus leniusculus, invasive crayfish) and prey (Gammarus pulex, amphipods) have on the ingress of fine sediment into gravel substrates and therefore on available interstitial refugia? (2) Do prey taxa seek refuge from (invasive) predators in the form of vertical movement into subsurface sediments? and (3) How does fine sediment ingress influence predator-prey interactions and prey survival through predator avoidance behavior. Here, we provide direct evidence demonstrating that fine sediment ingress into gravel river beds can be facilitated by zoogeomorphic activity with P. leniusculus increasing the infiltration of fine sand particles (but not coarse sand) during foraging activities. Predator-prey interactions were found to be a primary factor mediating zoogeomorphic activity, with the isolation of crayfish from prey (G. pulex) leading to increased fine sand ingress. When present with signal crayfish, G. pulex displayed vertical avoidance behavior, entering subsurface substrates to evade predation by P. leniusculus. Coarse sand treatments resulted in higher predation rates of G. pulex, most likely due to clogging of interstitial pore spaces between gravels limiting the effectiveness of the prey's vertical avoidance behavior strategy. A new conceptual model that captures the interactions between predator, prey, zoogeomorphic processes and habitat availability is presented. This model highlights how predator-prey interactions can be strongly mediated by dynamic bi-directional interactions between organisms and the physical environment they inhabit as ecological and geomorphological processes are intrinsically linked.