Depth-integrated net primary production (NPP) and bacterial secondary production (BSP) fluctuated between 49 and 1215 and 36 and 150 mg C m(-2) d(-1), respectively, with higher rates in oceanic waters. At a time series station located close to the Baker River mouth, the average NPP was lower (average 360 mg C m(-2) d(-1)) than at more oceanic stations (average 1063 mg C m(-2) d(-1)), and numerically dominated (45%) by the picoplankton (<2 mu m) and nanoplankton (2-20 mu m) size fractions. The high average vertical carbon flux (234 mg m(-2) d(-1)) and high export production (65% of the NPP) support the idea that Patagonian fjords may behave as a net sink for CO2 during the productive (spring) season. Trophic fluxes near the head of the fjords, with oligotrophic low-salinity waters, were dominated by heterotrophic nanoflagellates (HNF) and small copepods (52 mg C m(-2) d(-1) each), suggesting that the microbial food web is the main trophic pathway in these environments. (C) 2013 Elsevier Ltd. All rights reserved.