Description: Bacteria play a crucial role in the marine carbon cycle. To better understand the impacts of ocean warming and acidification on marine carbon cycling, natural analogues for future ocean conditions have gained increasing popularity. Here, 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 (Cowley Islet; CoI), 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. At each site, we collected data from five (four at RoR) spatially independent subsites. Physical water parameters were measured in situ using a Eureka Manta probe. Inorganic nutrient concentrations were determined on a continuous flow injection analyzer. Particulate (POC) and dissolved organic carbon (DOC) were quantified as difference in filter weight after filtration using pre-combusted GFF filters and via the high-temperature combustion technique, respectively. Transparent exopolymers (TEP) were determined using the xanthan equivalent method. This data is available in the 'water chemistry' data set and is directly linked to the sequence data obtained from free-living and particle-attached bacterial communities (ENA PRJEB27168). The table of operational taxonomic units (OTUs) and their assigned taxonomy that were generated after the bioinformatic sequence processing are likewise included in this data submission. Additional to the environmental sampling, a rolling tank experiment was conducted to assess the potential of the water to form larger marine aggregates. Estimated aggregate volume in the rolling tank from each subsite is available in the 'Aggregates analysis' data set. All scripts (R and bash code) that were used for the analysis of the data deposited here and on ENA are attached to the submission. Both RoR and BoC exhibited temperatures elevated by 1 - 1.5°C compared to the reference site. RoR further experienced reduced pH between 6.8 and 7.4. We observed pronounced differences in organic carbon pools (POC, DOC, TEP) at each of the three sites, with highest particulate organic carbon concentrations and aggregate formation at BoC. Bacterioplankton at BoC was dominated by opportunistic copiotrophic taxa, such as Alteromonas and Roseobacter, known for phytoplankton blooms, as opposed to oligotrophic taxa dominating the reference site, such as SAR 11. We presume that bacterial communities were rather influenced by the availability of organic carbon than directly by pH or temperature. Our results highlight the difficulty of establishing natural analogues, and suggest that at the time of sampling the selected sites were not suitable to represent future ocean conditions. Nevertheless, we provide a comprehensive characterization of organic carbon pools and bacterioplankton communities around the Galapagos Archipelago.