Habitat-forming species can influence mortality on associated species via altering structural and non-structural abiotic conditions. Importantly, these effects can occur simultaneously and in opposite directions, although how they contribute to the net outcomes for predator-prey interactions remain unexplored. Seagrasses often have positive effects on associated fauna because their structure directly reduces predator encounter rates. However, we identified a 'risky' behaviour (shallower burial) in an infaunal bivalve at a high seagrass cover--likely induced by non-structural abiotic change--suggesting positive effects may be outweighed by risky behaviours. We determined whether the physical structure of the seagrass interacted with burial behaviour of clams to determine the predation and non-predation mortality and whether these interactions were mediated by the cover of the seagrass. Surveys on an intertidal sand flat in Tasmania, Australia showed that the highest densities of a dominant bivalve, Katelysia scalarina, occurred at low (33%) seagrass cover, but the lowest densities and the highest proportion of unburied clams occurred at high (100%) cover. A field experiment manipulating burial depth, seagrass cover and predator access demonstrated that unburied clams suffered very high predation and non-predation mortality compared to buried clams (~4x higher), which outweighed any positive effects of the seagrass structure in reducing predator access. Being unburied also had non-lethal consequences with surviving unburied clams having a reduced tissue biomass compared to buried clams. In this system, predation was driven by the availability of prey when they undertake a risky behaviour (shallow burial). However, significant changes in behaviour may only occur once a threshold of habitat-former density is reached. In this instance, changes in behaviour were likely due to seagrass effects on sediment redox potential, which decreased significantly above 33% seagrass cover. Our findings demonstrate that the negative effects of a habitat-former on the behaviour of associated species, via alteration of non-structural abiotic conditions, can outweigh any positive effects provided by increasing habitat structure as is commonly reported for habitat-formers.