Geophysical controls on metabolic cycling in three Patagonian fjords

•Fjord function resolved via high-res sampling, open-water methods and models.•Metabolic balance in tide- and wind-driven fjords depends on regional connectivity.•Synoptic winds drive upwelling and corollary processes due to mid-fjord river input.•Salt fingering in Comau Fjord drives nutrient transport and may regulate metabolism.•Climate change will impact carbon storage and aquaculture resilience in fjords. Biogeochemical cycling in fjords underpins crucial environmental and economic functions including carbon sequestration and food security, and a fundamental understanding of the controls on these cycles is essential for sustainable management of fjords that are facing increasing climate and anthropogenic stressors. However, the interaction of external forcing and local geomorphology in fjords leads to complex coupling that is challenging to measure using traditional methods, particularly in a connected coastal system like the Chiloe Inland Sea (CIS) in northern Patagonia. This study resolves key functional differences between the three major fjords (Reloncaví, Comau and Reñihue) in the CIS using high-resolution sampling of surface waters integrated with regional oceanographic and meteorological observations, models and historic data. The dominant geophysical control varied among the three fjords: river input in Reloncaví Fjord, synoptic winds in Comau Fjord and tidal forcing in Reñihue Fjord. Variable geomorphic characteristics, e.g., orientation and the location of the riverine input, resulted in contrasting physical-metabolic responses between fjords to otherwise similar meteorological and oceanic forcing conditions. Each fjord’s relative location and degree of connectivity to the CIS influenced its internal metabolic balance over synoptic to seasonal scales. In Comau Fjord, the salt fingering form of double diffusive mixing was linked to vertical density structure and wind forcing in the northern CIS; consistent trends in historical data suggest that salt fingering may be an important mechanism for delivery of nutrients to the euphotic zone. The highest metabolic rates in the study region occurred in Reñihue Fjord and were linked to vertical mixing of nutrient-rich waters to the surface in the central CIS. Climate change is predicted to result in decreasing river discharge and weakening zonal winds in northern Patagonia. Therefore, the functional relationships observed in this study imply-two key impacts of these altered forcing conditions in coming