Although planktonic diatoms are one of the most abundant taxonomic groups in coastal wetlands, their assemblages have not been used to determine the environmental health of these ecosystems. Studies of ecosystem environmental health have been based on other taxonomic groups; we propose that diatom genera diversity represents a viable alternative for this purpose. Thus, our aim was to determine the alpha and beta diversities of the planktonic diatom assemblage present in Caulin Bay, Chiloe Island,southern Chile, during the austral winter and spring of the years 2012 and 2014. Inasmuch Caulin Bay is an important site for aquatic bird observation and conservation, hunting is prohibited on a national scale and, internationally, the site has been declared an Important Bird and Biodiversity Area (IBA). Our results indicate different diversities between sampling stations, but not between the years studied. In total, we recorded 53 diatom genera, of which the most abundant were Coscinodiscus (21.99%) and Cocconeis (16.23%). The study area presented high genera diversity and beta diversity indicated that Caulin presents a low level of heterogeneity and is a low genera replacement environment. Consequently, we infer that Caulin Bay is productive and environmentally stable ecosystem. This leads us to conclude that diatom diversity determination is a viable alternative to establish aquatic ecosystem environmental health and we recommend that future conservation strategies be established for Caulin Bay.