Here we present the first reconstruction of changes in surface primary production during the last century from the Puyuhuapi fjord in southern Chile, using a variety of parameters (diatoms, biogenic silica, total organic carbon, chlorins, and proteins) as productivity proxies. Two sediment cores from the head and the center of the fjord were analyzed and compared to gain insights on past changes in productivity in these two different depositional environments. Higher sedimentation rates found at the head of the fjord result from the combination of a shallower water column and a restricted circulation by the occurrence of a sill. Additionally, sediment mixing depths estimated from 210Pb data suggest that suboxic conditions may dominate the bottom water and the sediment–water interface in this location. Productivity of the Puyuhuapi fjord during the last century was characterized by a constant increase from the late 19th century to the early 1980s, then decreased until the late 1990s, and then rose again to present-day values. The influence of rainfall on productivity was most noticeable during periods of low rainfall, which coincided with decreased overall productivity within the Puyuhuapi fjord. Simultaneous variations in productivity and rainfall in the study area suggest that marine productivity could respond to atmospheric–oceanic interactions at a local scale. At a regional scale, marine productivity of the area may be related to other large-scale processes such as the El Niño Southern Oscillation.