The urban waterfronts of submerged heritage cities offer great opportunities and space for bringing nature into cities, they provide inspiration for closer relationships between nature, heritage sites and society. On the other hand, these urban waterfronts suffer from disconnection between nature and culture in heritage conservation practices. This disconnection has negatively impacted not only on the heritage sites, but also on ecosystems, citizens’ health, and wellbeing. Biophilic urbanism is an approach that seeks to integrate nature into urban waterfront spaces, creating healthier and more liveable cities. This paper aims to fill the gap between nature and cultural in conservation practices by adopting the concept of biophilic urbanism, which provides a valuable tool for conservation the urban waterfronts of submerged heritage cities, in addition to the balance conservation with development and create more resilient waterfront communities. The paper examines case studies of urban waterfronts in (Zadar, Croatia), (Baia, Italy), and (Abo Qir, Egypt). The results indicate the necessity of modifying Abo Qir’s urban waterfront development plan to incorporate indicators of Biophilic urbanism. This adjustment is crucial in order to ensure that future generations inherit healthy and vital living spaces, in addition to preserve Abo Qir’s significant submerged heritage cities.