This study aims to closely explore the potential of sustainable climate smart aquaculture (CSA) technologies, innovations and management practices (TIMPs) and sustainable fisheries management practices to reduce GHG emissions in Kenya while increasing climate resilience and boosting food production. In this paper, we used a mixed-methods approach for a systematic review process and a multistakeholder workshop that were conducted to explore future scenarios on the transformation and development of aquatic food systems. In Kenya, priority areas with high potential for low-GHG emissions in aquaculture include (i) selective breeding, (ii) solar powered recirculating aquaculture systems (RASs), (iii) aquaponics, (iv) novel fish feed alternatives, such as biofloc technology (BFT), periphyton technology (PPT) and sustainable biowaste management using black soldier fly larvae (BSFL), (v) integrated agriculture–aquaculture (IAA) and integrated multitrophic aquaculture systems (IMTAs). For capture fisheries, the main objective is to reduce fuel combustion and bottom contact while outlining the prospects of using fuel alternatives and limiting fishing efforts to reduce GHG emissions in the sector. Furthermore, post-harvest technologies support the addition of fish value and minimize food waste, while optimized processing efficiency reduces the release of GHG emissions. This paper recommends the formulation of supporting public and private sector policies that include incentives and capacity enhancement of local communities to encourage adoption and upscaling of CSA technologies. This will support the transition to low-GHG aquaculture production in Kenya’s aquaculture sector. In doing so, it will enhance food security while minimizing the negative impacts of fisheries and aquaculture on the environment.