We investigated three contrasting oceanographic settings in the Galapagos Archipelago regarding their suitability to represent future ocean conditions in research on organic carbon pools and bacterioplankton communities. Compared to a reference site representative of ambient pH and temperature, we studied a submarine CO2 vent at Roca Redonda (RoR), and an upwelling site at Bolivar Channel (BoC) subjected to a weak El-Nino event at the time of sampling in October 2014. We recorded physico-chemical parameters, and quantified particulate and dissolved organic carbon, transparent exopolymeric particles, and the potential of the water to form larger marine aggregates. Free-living (filtered on 0.2µm) and particle-attached (filtered on 3µm) bacterial communities were assessed via 16S rRNA gene sequencing on Illumina MiSeq (V3V4 hypervariable region).