Abstract <p>The article presents the results of measurements of nutrients (including silicates, inorganic and organic forms of nitrogen, and phosphorus) in waters of the bays of the Shantar Archipelago (SA) in July 2016 and September 2022. It was found that photosynthesis predominantly removes inorganic forms of nitrogen and phosphorus from the surface waters of SA bays. River runoff leads to enrichment of SA waters in silicates and dissolved organic carbon. It was revealed that spawning salmon play an important role in enriching the apex of Akademii Bay with total phosphorus and nitrogen. Removal of nutrients from waters of SA bays by salmon fingerlings migrating to the open part of the Sea of Okhotsk in autumn has been shown. Application of the two-layer LOICZ model to SA waters showed that the main source of different forms of nitrogen and phosphorus are bottom waters of the open part of the Sea of Okhotsk (80–90% of the total nutrient flux into the bays). The model is based on the concept of estuarine water circulation, which maintains a stable long-term nutrient content in waters of SA bays, which are geographically isolated from the Sea of Okhotsk. It is suggested that salt marshes along the SA coastline may be an important source of nutrients and organic matter production. The main runoff of nutrients from the bays is the directed flow of the upper layer of water from the bays to the open sea.</p>