Recent observations suggest an arctic climate system in broad transformation, yet the regional marine-ecosystem response is poorly known. Here, we develop and analyze a comprehensive biogeophysical dataset of key water constituents – chlorophyll (chl), suspended sediments (sm) and dissolved organic matter (doc) – using satellite ocean-color data from the White Sea in the Russian Arctic, for the period 1998–2004. The revealed changes in chl, sm and doc are more pronounced in the bays (e.g., the southeastern bay trends are −20%, +18% and +11%, respectively) than in the central basin (−5%, +5% and +3%, respectively). The chlorophyll decreases reflect the impact of enhanced runoff on sm and doc, which make the water more turbid and less favourable for phytoplankton growth, in contrast to other arctic seas where increased phytoplankton is expected. This case study supports our hypothesis that the marine ecosystems of semi-enclosed arctic shelf seas respond rapidly to climate change and are thus particularly vulnerable to future global warming.