The present study critically analyses peer-reviewed literature addressing the potential of halophytes to remediate nutrient-rich effluents from marine and coastal aquaculture, as well as the potential for their economic valorization, from human consumption to an untapped source of valuable secondary metabolites with pharmaceutical potential. The growing body of evidence discussed in this review supports the perspective that halophytes can become a new source of nutrition and other high-value compounds and be easily incorporated into saltwater-based integrated multi-trophic aquaculture (IMTA) systems. In this context, halophytes act as extractors of dissolved inorganic nutrients, primarily nitrogen and phosphate, usually wasted in marine aquaculture farms. Phytoremediation using halophytes has been proven to be an efficient solution, and several ways exist to couple this practice with land-based marine aquaculture systems, namely through constructed wetlands and aquaponics. Focusing research on ecosystem-based approaches to aquaculture production will provide valuable data for producers and policy makers in order to improve decision making towards a sustainable development of this economic sector. Ecointensification of aquaculture through IMTA will potentially increase the overall productivity and resilience of the sector, and halophytes, in particular, are on the verge of becoming key players for the diversification and promotion of land-based IMTA. This work specifically documents the uncharted potential of Halimione portulacoides, an important halophyte in European salt marsh ecosystems, as a new extractive species for IMTA.