The role of environmental-stress gradients in driving trophic processes like grazing, has potential to shape ecosystem responses to environmental change. In subtidal seagrass systems, however, the variation in top-down processes along stress gradients are poorly understood. We deployed herbivory assays using the five most common seagrass species of Shark Bay, to determine whether herbivory pressure changed across a salinity-stress gradient from oceanic (38 PSU) to hyper-saline (51 PSU) conditions. Seagrass tissue removed from herbivory assays by fishes decreased as environmental stress increased, and herbivores consumed greater amounts of tropical seagrass species compared to the temperate species that dominate seagrass cover in Shark Bay. This heightened consumption was correlated with enriched seagrass nutrient concentrations. Our work suggests there’s a fundamental relationship between trophic interactions and environmental conditions within complex marine settings. Abiotic stressors like salinity directly impact seagrass communities physiologically; however we show that salinity stressors also shift biotic interactions, indirectly influencing grazing rates and thus having a greater effect on seagrasses than physiological impacts alone. In Shark Bay where restoration efforts are being employed to address large scale loss of seagrasses, the relationship between herbivory pressure and salinity-stress could therefore prove crucial to restoration success.