This study investigates the geochemistry of soft, organic-rich brackish-water surface sediments in the Archipelago Sea (SW Finland). The area is one of the world’s largest archipelagos, and, although it is scarcely populated, frequent ship and boat traffic along with fish farming occurs. From 76 sites, 47 chemical elements were determined after aqua regia digestion. Other parameters determined were grain size, water, organic and nitrogen contents. At sampling, the sediments were visually classified into groups representing oxic, anoxic and fluctuating (intermediate) oxic seafloor conditions. The results show that the element concentrations are quite similar to other studies in the region but with clear signs of lower anthropogenic loading. Point source pollution was identified in one sample taken nearby a fish farm and a cable ferry. This site was strongly enriched in Cu, Zn and Sn derived from chemicals used in either, or both, activities at the site. Overall, the sediments can be divided into two groups that separate chemically and geographically. One group contains more fine-grained sediments that occur near shore, while the other group contains more anoxic, organic and sulfur-rich sediments occurring more offshore. The second group is interpreted to reflect material reworked from previous deposits as a result of shoaling of the area due to glacio-isostatic land uplift. The visual classes were included in both partial least squares regression (PLSR) and PLS discriminant analysis. These analyses showed that the oxic and anoxic seafloor sediments can be predicted from the chemical variables and grain-size distribution.