Carbon isotopes and C/N ratios are frequently used to separate allochthonous and autochthonous organic matter input into marine shelf sediments. We test the applicability of this approach for the sediment record from Comau Fjord in southern Chile (42°S) with the aim to reconstruct carbon and nitrogen mass accumulation rates and to determine their allochthonous and autochthonous sources for the last century. Comparisons with isotopic and geochemical signatures of potential organic matter sources demonstrate that mixtures between terrigenous soil and peat on the one hand and marine planktonic organic matter on the other hand readily explain variations of organic carbon (δ13Corg) and nitrogen (δ15N) isotopes as well as in C/N and N/C ratios and explain differences in absolute values of these parameters along a transect of cores. Nitrogen mass accumulation rates, calculated from δ15N and C/N ratio, and carbon mass accumulation rates, calculated from δ13Corg and N/C ratios of terrigenous organic matter, varied considerably less compared to those of autochthonous planktonic organic matter. Autochthonous carbon accumulation rates increased from between 1.2 and 5.2 g m−2 a−1 at the beginning of the last century to values between 21.5 and 29.9 g m−2 a−1 around the turn of the millennium. Even if the highest amount of diagenetic degradation is considered the mass accumulation rates increased by at least a factor of 2 within the last decades of the 20th century. The reasons for such a shift in primary productivity are discussed 1) in terms of recent climatic change in northwestern Patagonia possibly having lowered fluvial inflow into Comau Fjord and 2) in relation to anthropogenic eutrophication by rapidly expanding aquaculture. Given that allochthonous mass-accumulation rates remained fairly constant, we conclude that anthropogenic eutrophication caused by aquaculture is the more likely explanation for increased carbon and nitrogen accumulation rates in the last two decades in Comau Fjord. Moreover, a new proxy for marine productivity versus clastic terrigenous input (Br/Ti ratio) is suggested for the Chilean fjord environment.