Environmental disturbances can be monitored using sentinel species. This study presents 30 temporally explicit metagenomes and 166 metagenome-assembled genomes (MAGs) from the gut of the South American sea lion (Otaria flavescens) from the Comau Fjord in Patagonia. These genomic resources provide tools to understand whether variations in gut microbiome composition and gene content might reflect environmental disturbances from salmon farming and other anthropogenic impacts in this unique coastal ecosystem.