The capacity of many macroalgae to rapidly absorb soluble inorganic nutrients and convert them into primary biomass provides opportunities for their use in the bioremediation of nutrient-enriched waters. Marine-based macroalgal cultivation has the potential to target diffuse source nutrient discharges and produce valuable bioproducts such as fertiliser, soil conditioning agents and agricultural feed additives and phycocolloids. Whilst macroalgal diversity offers benefits for improving and maintaining healthy marine ecosystems, it also presents a challenge for determining the best candidate species for cultivation as a nutrient biofilter and, ultimately, a source of bioproducts. We developed and applied a multi-criteria selection model to identify likely candidate macroalgal species for cultivation in Queensland’s coastal waters for biofiltration and bioproduct development, focusing on native species and product development for the agronomical and horticultural sectors. From a species database of 1380 macroalgal species, candidates were initially selected based on their regional abundance, distribution and morphological characteristics considered amenable to in-situ cultivation and harvesting. From a resulting shortlist of 17 species, five systematic literature searches were applied to identify biofilter potential, bioproduct potential and current cultivation status. Of the shortlisted species, Ulva lactuca, Gracilaria edulis and Hypnea cervicornis ranked most highly in the multi-criteria analysis, with several other species showing good potential, but requiring further investment in understanding key biological processes and the development of cultivation protocols.