Grazing and burrowing organisms usually homogenise microalgal mats that form on benthic sediments of many aquatic ecosystems. In the absence of this disruption, microalgal mats can accrete laminated deposits (stromatolites). Stromatolites are rare in modern coastal ecosystems, but persist at locations where metazoans are largely excluded. This study aimed to assess the trophic structure at stromatolite locations where metazoans co-occur, to determine the grazing influence exerted by the metazoans on the stromatolite-forming microalgae (cyanobacteria and diatoms). Stable isotope signatures (δ13C and δ15N) were used as food-web tracers and dietary composition of consumers was calculated using source mixing models. Results clearly demonstrate that the dominant macrofaunal grazers do not utilise stromatolite material as a food resource, but rather subsist on autochthonous macroalgae. For instance, the mean (±SD) dietary composition of two of the most abundant grazers, Melita zeylanica (Amphipoda) and Composetia cf. keiskama (Polychaeta), consisted of 80 ± 11% and 91 ± 7% macroalgae, respectively. This suggests that the stromatolite-forming benthic microalgae are not disrupted significantly by grazing pressures, allowing for the layered mineralisation process to perpetuate. Additionally, grazers likely have a restrictive influence on pool macroalgae, maintaining the competitive balance between micro- and macroalgal groups.