Ecological processes function to structure the species composition and dynamics of ecosystems . However, habitat destruction and fragmentation, eutrophication, and overharvesting can have detrimental effects on the scale and distribution of these processes and the species that provide them. Here we aim to demonstrate a method for prioritizing conservation efforts for the protection of critical ecosystem functions. Algae assays were deployed in seagrass beds across Moreton Bay, Queensland to determine herbivory. We found that the abundance of a commercially harvested herbivorous fish species was a suitable surrogate for herbivory in seagrass meadows within a disturbed coastal ecosystem. Species distribution models for this species highlight seagrass meadows closest to anthropogenic disturbance were the most important for the abundance of this species, and thus suppressing algal overgrowth within seagrass meadows through herbivory. Critical habitats were predominantly located outside of current conservation boundaries and therefore represent priority areas for conservation. This is the first study to highlight that conservation prioritization for ecosystem functions could be focused in areas that may receive the most anthropogenic disturbance and may have previous been deemed a poor choice for conservation prioritization.