The Gulf of Nicoya is a tropical estuary located on the Pacific coast of Costa Rica. Changes in river inflow during dry and rainy seasons make the gulf a dynamic ecosystem. During the rainy season, freshwater input and organic matter discharge cause environmental gradients that affect the structure of the bacterioplankton communities so that at the beginning of the rainy season, the surface layers of the gulf are relatively homogeneous; the opposite occurs during the dry season, where is observed more significant heterogeneity in the structure of the bacterioplankton communities along the surface of the gulf. The determination of these changes in microbial diversity and abundance throughout the year are insights for understanding the dynamics of the ecosystem and establishing indicators for the development of mariculture projects, such as oyster farming.