There is a relative lack of research, targeted models and tools to manage beaches in estuaries and bays (BEBs). Many estuaries and bays have been highly modified and urbanised, for example port developments and coastal revetments. This paper outlines the complications and opportunities for conserving and managing BEBs in modified estuaries. To do this, we focus on eight diverse case studies from North and South America, Asia, Europe, Africa and Australia combined with the broader global literature. Our key findings are as follows: (1) BEBs are diverse and exist under a great variety of tide and wave conditions that differentiate them from open-coast beaches; (2) BEBs often lack statutory protection and many have already been sacrificed to development; (3) BEBs lack specific management tools and are often managed using tools developed for open-coast beaches; and (4) BEBs have the potential to become important in “nature-based” management solutions. We set the future research agenda for BEBs, which should include broadening research to include greater diversity of BEBs than in the past, standardising monitoring techniques, including the development of global databases using citizen science and developing specific management tools for BEBs. We must recognise BEBs as unique coastal features and develop the required fundamental knowledge and tools to effectively manage them, so they can continue providing their unique ecosystem services.