The New Zealand aquaculture industry is based primarily on the production of Greenshell™ mussels, Chinook salmon and Pacific oysters. The industry is primed for development and is anticipating increasing its export earnings to NZ$3 billion by 2035. To achieve this target and retain its ‘clean and green’ image, the industry must be able to demonstrate that its practices are sustainable. Integrated multi‐trophic aquaculture (IMTA) systems provide an avenue to address this challenge, with most of the work in New Zealand focusing on the integration of low trophic level high‐value species such as sea cucumbers and seaweeds with mussels, providing environmental bioremediation and provision of valuable secondary products (nutraceuticals and pharmaceuticals). Ecophysiological, hydrodynamic and benthic diagenesis models have been developed to underpin this IMTA research into sustainable farming designs. However, many regulatory barriers are still in place, which together with the current lack of investment, market security for these new products and associated operational costs form the main constrains to development. Nevertheless, the recent emergence of aquaculture fora where industry, researchers, and regulators meet to discuss future research and development has invigorated interest in diversification of the sector, inclusive of IMTA within existing coastal areas and upcoming land‐based and open‐ocean operations.