Metabarcoding data in the coastal lagoon located on the east coast of Korea.

We examined seasonal and spatial changes in bacterial communities in two Korean coastal lagoons, such as Gyeongpoho (open) and Hyangho (intermittently open), using 16S rRNA gene metabarcoding. Our study found that hydrology and geomorphology strongly influence microbial composition. Gyeongpoho showed more variation due to constant seawater exchange, while Hyangho had a more stable community under freshwater dominance. Salinity changes, especially after monsoon events, affected microbial diversity and dominant taxa. Heterotrophic bacteria were prevalent, likely due to their role in nutrient cycling. This study revealed that bacterial communities are sensitive to hydrological shifts, offering insights into how lagoon ecosystems respond to environmental and climate changes.