Environmental sustainability and global food system security are at risk due to climate change and ecosystem degradation. Innovative integrated algae-based aquaponics systems promise a potential pathway for improved resource use, adaptation to climate change, and ecosystem restoration. This chapter delves into the synergies between aquaponics and algae in advancing sustainable efforts in aquaculture and agriculture. Algae play several crucial roles in ecosystem restoration, including carbon sequestration, bioremediation, and biodiversity conservation. It supports environmental restoration through cutting-edge methods that may help absorb nutrient run-off from farming and mitigate climate change. Water efficiency is further enhanced by incorporating algae into aquaponic systems, along with nutrient recycling and climate resilience. Aquaponics is the closed-loop farming of aquaculture and hydroponics, which minimizes waste and water use to produce food sustainably. Incorporating algae into these systems not only improves nutrient availability and acts as a natural biofilter but also supports the health of both fish and crops while delivering essential ecosystem services. Combining algae with aquaponics offers a viable and scalable option to adapt to climate change by lowering environmental footprints, boosting ecosystem resilience, and safeguarding food and energy security. However, financial constraints, potential environmental risks, and technological obstacles limit the large-scale implementation of algae-aquaponics systems. Overcoming these hurdles will require coordinated multidisciplinary research, policy support, and technological innovation. This chapter concludes by outlining future research directions and emphasizing the urgent need for legislative initiatives to scale algae-aquaponics systems as a sustainable solution to pressing global environmental and agricultural challenges.