Aquaculture is an ancient practice that has gradually evolved over millennia, often drawing from traditional knowledge, the curiosity and needs of farmers, their positive experiences and mistakes, as well as collaborative efforts. Consequently, it has expanded over centuries, integrating with the natural (biotic and abiotic factors of ecosystems), social, economic, and cultural contexts. However, intensive aquaculture has led to a decline in fish biodiversity and abundance in both marine and freshwater ecosystems worldwide, impacting food security. The scientific community has highlighted the urgent need to address the climate change emergency and the biodiversity crisis while promoting sustainable aquaculture. The widespread decline of fish populations has prompted the development of various ecosystem-based management strategies and nature-based solutions (NbS). These approaches aim to enhance the sustainability of harvests by ensuring ecosystem resilience and improving overall ecosystem health. Recognizing the significance of aquaculture alongside other critical issues such as zero hunger, poverty alleviation, climate change, clean water and sanitation, and marine life preservation, the United Nations introduced the 2030 Agenda for Sustainable Development, a comprehensive framework for global peace and prosperity. By adopting this agenda, countries have shown a strong commitment to making bold and transformative changes toward a more sustainable and resilient future. This study reviews the current state of aquaculture, examines its effects on fish biodiversity, and discusses ecosystem-based management strategies and nature-based solutions for sustainable aquaculture. It is noteworthy that global aquaculture production is largely dominated by a limited number of species, which could undermine resilience to future challenges like anthropogenic pressures, climate change, and emerging diseases.