Microbes play an important role in coastal and estuarine waters where they influence biogeochemical cycling and respond to environmental changes. This study presents 93 metagenomes and 677 metagenome-assembled genomes (MAGs) from Comau Fjord, Patagonia (42°S), to understand the microbial dynamics and their response to anthropogenic disturbances. These data represent a spatially explicit transect spanning 35 km and temporally explicit samples collected from 2016 to 2019, providing insights into microbial community structure and function in a dynamic coastal environment.