Processes, such as sea level rise, that alter tidal inundation regimes have the potential to modify the structure of seagrasses and their dense and diverse faunal communities. This study tested the hypothesis that seagrass-dwelling invertebrate communities would vary across a tidal inundation gradient as a result of direct effects of tidal inundation and indirect effects, arising from changes in seagrass morphology across this gradient. First, we conducted mensurative sampling across tidal inundation gradients to assess how above- and below-ground seagrass biomass, and epi- and infaunal invertebrate communities co-varied with depth. Second, we ran a manipulative field experiment, utilising artificial seagrass rhizomes of varying morphologies, to separate out direct effects of tidal inundation on infaunal communities from indirect effects arising from changes in seagrass root morphology. Mensurative sampling revealed that the abundance and taxon richness of seagrass epi- and infauna, and the above- and below-ground biomass of seagrass each increased with depth across a tidal elevation gradient extending from the high intertidal to the shallow subtidal. The manipulative experiment revealed that the relative importance of direct and indirect effects of tidal inundation in determining the distribution and abundance of infauna were taxon-specific. In general, however, the facilitative effects of rhizome structure were more evident at the intertidal compared to the subtidal elevation. Our results indicate that changes to tidal inundation regime will affect seagrass-dwelling macroinvertebrates through a combination of direct and indirect effects. Therefore, future changes in tidal inundation should be taken into account in developing conservation plans for protecting seagrasses and the biodiversity they sustain.