Wild aquatic birds are vital to aquatic ecosystems, fulfilling roles as pollinators, seed dispersers, and facilitators of nutrient cycling. Yet, their populations face significant threats from infectious diseases such as avian influenza and botulism, which risk ecological disruption and biodiversity loss. Conventional disease management strategies often fall short due to inefficacy or unintended environmental consequences, prompting the exploration of innovative alternatives. This chapter examines the potential of nano-based antimicrobial agents including silver, copper, and zinc nanoparticles as targeted solutions for disease control in these populations. By taking advantage of their distinctive physicochemical traits, such as a high surface-area-to-volume ratio and the ability to specifically target pathogens, these agents fight microbes through various mechanisms including the production of reactive oxygen species, disruption of cell membranes as well as interference with the genetic material. Their advantages over traditional antimicrobials include enhanced efficacy, reduced resistance development and broad-spectrum activity. However, ecological concerns stick with their environmental behaviour including long-distance transport, aggregation, persistence, and bioaccumulation risks within aquatic food webs. These factors offer emphasis to possible impacts on non-target species as well as ecosystem integrity, ultimately, demanding thorough ethical evaluation and risk assessment frameworks. The chapter emphasizes an urgent need for inter-disciplinary research to address gaps in long-term ecological effects, species-specific vulnerabilities, and the expansion of globally synchronized regulatory standards. By balancing innovation with environmental stewardship, nano-based antimicrobials could come forward as a sustainable tool for safe-guarding avian health and aquatic ecosystem resilience.