One of the most important factors controlling fjord primary production in southernmost Patagonia is the variability in the thermohaline structure of the water column. In the present-day environment, thermal stratification is mostly related to freshwater input and in particular, the seasonal melting of glaciers. Here we assess whether this relation between fjord productivity and freshwater input holds true for the Holocene, using a sediment record from the central basin of the Strait of Magellan (core MD07-3132, 53°44.17′S; 70°19.03′W, 301 m). Our approach relies on a proxy-based reconstruction of fjord sea surface temperature (alkenone SST), paleosalinity, freshwater input, and paleoproductivity. The results indicate that, during the early Holocene, the accumulation rate (AR) of marine organic carbon was low (< 20 kg m− 2 kyr− 1), most likely due to high freshwater contribution resulting in low salinity and low SSTs. After 8.5 kyr BP and during the mid and late Holocene all the productivity proxies increase. The AR's of marine organic carbon (~ 30 kg m− 2 kyr− 1), biogenic CaCO3 (~ 60 kg m− 2 kyr− 1) and biogenic opal (425 kg m− 2 kyr− 1) reached the highest values during the last millennium. This increase was probably driven by the marine transgression where marine macronutrient-rich waters entered into the central basin, while lowered precipitation and decreased meltwater input contributed to increase the basin's SSTs and salinity. The late Holocene rise in productivity was interrupted by a low salinity phase between 3.2 and 2.2 kyr BP, during which productivity returned to early Holocene conditions in response to increased input of glacial clays, as suggested by high values of K/Si ratio (~ 1.2). Our results indicate that meltwater contribution from glaciers plays a crucial role in controlling fjord productivity on seasonal to millennial timescales.