Structural habitat complexity is a fundamental attribute influencing ecological food webs. Simplification of complex habitats occurs due to both natural and anthropogenic pressures that can alter productivity of food webs. Relationships between food web structure and habitat complexity may be influenced by multiple mechanisms, and untangling these can be challenging. We investigated whether (1) size spectra vary across a gradient of habitat complexity in seagrass meadows and (2) structural complexity changes the importance of different primary producers supporting the food web (determined using stable isotope analysis) in the Great Barrier Reef World Heritage Area. We found that moderately complex meadows had much steeper size spectra slopes, caused by a higher abundance of smaller animals and fewer larger animals, while meadows on either end of the complexity scale (low and a single meadow with very high complexity) had shallower slopes, indicative of a more balanced distribution of animal sizes across the spectrum. We also found that the importance of epiphytic algae as a food source was high in most meadows, despite the increase in seagrass surface area on which epiphytes could grow. The consistent importance of epiphytic algae suggests that the changes in the availability of different potential food sources did not affect food web structure. Our findings indicate that food web structure may change with variations in structural complexity because of changes in the abundance of smaller and/or larger animals. Food web structure and food sources are important determinants of the dynamic stability of food webs. Size spectra analysis is already used as a monitoring tool for assessing populations of key fisheries species in commercial fishing operations, and thus, we recommend using size spectra as a proxy for assessing the structure of the food webs in different types of seagrass meadows. Size spectra may be a useful indicator of how different meadows provide for ecosystem services such as fisheries.