Cockles are bioengineers in seagrass and sediment habitats. Through bioturbation they can modify sediment properties and seagrass growth and survival, and when unburied their shells can provide a substrate for epibiont colonisation. Warming may influence ecosystem bioengineering by cockles by altering their density, morphology and/or behaviour, and by modifying seagrass traits that influence their ability to bury. In Lake Macquarie NSW, warm water discharge from power plants creates a thermal gradient across which hypotheses about effects of temperature can be tested at scale. We assessed differences in cockle and seagrass density, and cockle population size structure and burial between sites varying in temperature by 3oC. Cockle densities mirrored that of seagrass and were higher in cooler sites, yet cockles grew bigger in warmer environments. Irrespective of temperature, in bare sand, cockles tended to fully bury themselves in vertical positions. By contrast, in seagrass patches, they often stayed half buried or on the sediment surface, with fewer cockles buried at warmer than cooler sites. Colonisation of hard, exposed substrates was greater at warm than cool sites. Consequently, in seagrass beds, warming may shift the role of cockles from bioturbation to substrate provision, with potential implications for seagrass and community structure.