Estuaries are often seen as important filters between land and the sea for inorganic and organic nutrients. This paper aims at estimating the estuarine fluxes of dissolved inorganic nitrogen (DIN), dissolved inorganic phosphorus (DIP) and dissolved silicate for the major oligothrophic and pristine rivers running into the Bothnian Bay (BB) and the Bothnian Sea (BS), the northern subarctic subbasins of the Baltic Sea. Long-term data sets for these rivers and their estuaries as well as for the BB and BS were analyzed to assess whether these estuaries are sinks for inorganic nutrients. Most studied estuaries can be characterized as salt wedge estuaries with little exchange between the fresh seaward-flowing river water and the inward-flowing seawater. Estimates of water transit times ranged between 1 and 14 days. In most estuaries of the BB, N-depleted river water meets P-depleted seawater during the growth period. These findings were corroborated by mixing diagrams showing that the inner areas of the estuaries were N-depleted in summer. In the BS, on the other hand, both rivers and seawater were mostly N-depleted during summer. Thus, for most estuaries of this region of the Baltic Sea, primary productivity is presumably lower than or equal to that of offshore. The low productivity is also reflected in the sediments. The coastal sediments did not differ from the offshore stations in accumulation rates as well as the content of organic matter and nutrients, indicating that estuarine nutrient burial is not always higher as normally observed in other temperate systems. Finally, the estuaries of the pristine rivers in the northernmost part of the BB import DIN during summer, whereas the estuaries of the rivers in the BS import DIP during winter, from the sea.