Traditional aquaculture provides food for humans, but produces a large amount of wastewater, threatening global sustainability. The antibiotics abuse and the water replacement or treatment causes safety problems and increases the aquaculture cost. To overcome environmental and economic problems in the aquaculture industry, a lot of efforts have been devoted into the application of microalgae for wastewater remediation, biomass production, and water quality control. In this review, the systematic description of the technologies required for microalgae-assisted aquaculture and the recent progress were discussed. It deeply reviews the problems caused by the discharge of aquaculture wastewater and introduces the principles of microalgae-assisted aquaculture. Some interesting aspects, including nutrients assimilation mechanisms, algae cultivation systems (raceway pond and revolving algal biofilm), wastewater pretreatment, algal-bacterial cooperation, harvesting technologies (fungi-assisted harvesting and flotation), selection of algal species, and exploitation of value-added microalgae as aquaculture feed, were reviewed in this work. In view of the limitations of recent studies, to further reduce the negative effects of aquaculture wastewater on global sustainability, the future directions of microalgae-assisted aquaculture for industrial applications were suggested.

Microalgae, with their unparalleled capabilities for sunlight-driven growth, CO₂ fixation, and synthesis of diverse high-value compounds, represent sustainable cell factories for a circular bioeconomy. However, industrial deployment has been hindered by biological constraints and the inadequacy of conventional genetic tools. The advent of CRISPR-Cas systems initially provided precise gene editing via targeted DNA cleavage. This review argues that the true transformative potential lies in moving decisively beyond cutting to harness CRISPR as a versatile synthetic biology “Swiss Army Knife”. We synthesize the rapid evolution of CRISPR-derived tools—including transcriptional modulators (CRISPRa/i), epigenome editors, base/prime editors, multiplexed systems, and biosensor-integrated logic gates—and their revolutionary applications in microalgal engineering. These tools enable tunable gene expression, stable epigenetic reprogramming, DSB-free nucleotide-level precision editing, coordinated rewiring of complex metabolic networks, and dynamic, autonomous control in response to environmental cues. We critically evaluate their deployment to enhance photosynthesis, boost lipid/biofuel production, engineer high-value compound pathways (carotenoids, PUFAs, proteins), improve stress resilience, and optimize carbon utilization. Persistent challenges—species-specific tool optimization, delivery efficiency, genetic stability, scalability, and biosafety—are analyzed, alongside emerging solutions and future directions integrating AI, automation, and multi-omics. The strategic integration of this CRISPR toolkit unlocks the potential to engineer robust, high-productivity microalgal cell factories, finally realizing their promise as sustainable platforms for next-generation biomanufacturing.