ABSTRACTMicrobes play an important role in coastal and estuarine waters. We present 93 metagenomes and 677 metagenome-assembled genomes (MAGs) from Comau Fjord, Patagonia (42°S), to further understand the microbial dynamics and their response to anthropogenic disturbances. These data represent a spatially (35-km transect) and temporally (2016 to 2019) explicit data set.