Abstract Here we report on the seasonal productivity cycle at a fixed station in the Puyuhuapi Channel (44°S, 73°W), Chilean Patagonia. The analysis of in situ water column data and longer-term records of satellite-derived surface ocean color (Chl-a) highlighted two contrasting seasons. A more productive period occurred between August and April, where depth-integrated gross primary production (GPP) estimates ranged from 0.1 to 2.9 g C m−2 d−1, and a shorter, less-productive season lasted from May to July with GPP ranging from 0.03 to 0.3 g C m−2 d−1. Diatoms of the genera Pseudo-nitzschia, Skeletonema and Chaetoceros dominated the phytoplankton, and showed a pronounced seasonality greatly influenced by prevailing environmental conditions. Warmer waters were associated with high concentrations of Pseudo-nitzschia spp., while high abundances of Skeletonema spp. and Chaetoceros spp. were associated with fresher silicate-rich waters. A marked Skeletonema spp. bloom characterized the onset of the productive season in August 2008, and with some exceptions, the highest levels of GPP (1.5 to 2.9 g C m−2 d−1) were measured when Skeletonema dominated the phytoplankton community. Reduced production (low GPP) was observed during periods of increased discharge from the Cisnes River, whereas the “spring” diatom bloom (or late winter bloom in Puyuhuapi Channel) observed during August 2008 coincided with a ~50% drop in the freshwater discharge. We therefore suggest that periods of intensive freshwater Input, that increase the silicic acid concentrations in the upper layers, provide ideal growing conditions for diatoms as the freshwater flow subsequently recedes. Principal component analysis (PCA) suggests that a decrease in salinity, increase in silicic acid concentration, and growth of Skeletonema spp. and Chaetoceros spp., are probably key factors in the annual cycle of GPP in Puyuhuapi Channel.