Nutrient inputs from upwelling, ocean currents, advection, and terrestrial sources play a crucial role in driving primary production in Arctic fjords and coastal areas. This study analyzes more than two decades of field measurements across a terrestrial-river-coastal continuum in Arctic Greenland, showing how shifts in coastal inflows, glacial meltwater, and terrestrial inputs control changes in nutrient dynamics in the fjord. Our data indicate oligotrophication, with nitrate concentrations decreasing by ∼49% and phytoplankton biomass by ∼60% over the study period. These changes are associated with a ∼12% increase in catchment vegetation greening, which likely reduced terrestrial nitrate input to the fjord by ∼65%. Nutrient dynamics in the fjord were also influenced by inflows of fresher coastal waters, providing nitrate-poor, silicate-rich waters. Silicate concentrations in the fjord have risen by ∼115% over the past two decades, suggesting increased input from all these sources. Whether these patterns are unique to this fjord or representative of broader Arctic trends remains uncertain and our study highlights the need to further explore the cross-boundary ecological impacts of climate change on Arctic marine and coastal ecosystems.