Increasing use of the marine environment and changes in weather extremes from climate change are altering patterns of sediment deposition on benthic habitats. There is a need to understand behavioural responses to such stressors, especially in sessile species that are of conservation, ecological or commercial interest. We investigated how two biogenic reef-forming, epifaunal mussels, Modiolus modiolus (horse mussel) and Mytilus edulis (blue mussel) responded to gradual burial by sediment. Here we used experiments to assess behavioural strategies for surviving modest, but regular sediment deposition regimes (0.5, 1.0 or 1.5 cm d−1 of coarse, medium-fine or fine sediment for 2, 4, 8 or 16 days), that result in gradual burial. M. modiolus was only capable of maintaining contact with the sediment-water interface during slow rates of deposition for short durations (tested in fine sediment only). M. edulis, however, were capable of vertical migration through sediment in all experimental sedimentation rates, sediment fractions and durations, but the frequency of burial increased with increasing sedimentation rate and duration. In this study, the sediment fraction was not influential on the levels of burial observed in M. edulis. Inter-individual variation in the ability of M. edulis to vertically migrate was investigated to understand sub-lethal effects of exposure to sedimentation. In M. edulis a molecular approach was used to assess variation in the condition and protein turnover in tissues with different functional roles (gill, adductor and foot tissue). Concentrations of RNA in the muscular foot were positively associated with the frequency of burial and the total depth of burial, indicating that burial stimulates protein production, most likely associated with byssus production used in the burial escape response. These findings contribute to a better understanding of how mussels respond to, and survive gradual burial by sediment and provide insight into how ongoing changes in sediment dynamics may influence these ecologically and commercially important reef-building species. These findings can be used to assist in managing activities which may result in sedimentation around these important species.