Genomic facilities have revolutionized avian conservation, particularly for water bird species, over the last couple of years. Researchers can now investigate ecological trends, adaptive response and evolutionary paths of species which were not researched as deeply before using such facilities and newer techniques. Along with increasing threats of climate change to which wetland and coastal environments are susceptible, habitat loss and anthropogenic disturbance, genomics provides important insight into aquatic bird reaction to these stresses. This chapter deals with how genetic diversity, migratory behavior and climate stress resistance are being addressed through the implementation of novel genomic tools in the form of whole-genome sequencing, eDNA analysis and machine learning algorithms. Researchers are now discovering more about the population structure and even the potential future response of these birds to an environmental change. Genomic data can be utilized as an effective guide in recommending well-intentioned conservation measures like the safeguarding of migratory routes and breeding grounds when complemented by ecological data and spatial modeling. This chapter will demonstrate that genomics not only expands our scientific understanding but also offers specific advice on how to maintain aquatic bird populations’ diversity.