The Patagonian fjords have a clear potential to provide high-resolution sedimentary and geochemical records of past climate and environmental change in the Southern Andes. To improve our ability to interpret these proxy records, we investigated the processes that control fjord sediment inorganic geochemistry through a geochemical, mineralogical and sedimentological analysis of surface sediment samples from the fjords of Northern Chilean Patagonia. A simple Terrestrial Index based on measurements of salinity and Fraction of Terrestrial Carbon was used to estimate the terrestrial input/river discharge at each site. Our results demonstrate that, under the cold climate conditions of Patagonia, chemical weathering is weak and the inorganic geochemical composition of the fjord sediments is primarily controlled by hydrodynamic mineralogical sorting, i.e., the intensity of river discharge. Our results suggest that the distribution of Fe, Ti and Zr in surface sediments is controlled by their association with heavy and/or coarse minerals, whereas Al is independent of hydrodynamic processes. The elemental ratios Fe/Al, Ti/Al and Zr/Al are therefore well suited for estimating changes in the energy of terrestrial sediment supply into the fjords through time. Zr/Al is particularly sensitive in proximal environments, while Fe/Al is most useful in the outer fjords and on the continental margin. In the most proximal environments, however, Fe/Al is inversely related to hydrodynamic conditions. Caution should therefore be exercised when interpreting Fe/Al ratios in terms of past river discharge. The application of these proxies to long sediment cores from Quitralco fjord and Golfo Elefantes validates our interpretations. Our results also emphasize the need to measure Al-based elemental ratios at high precision, which can be achieved using simultaneous acquisition ICP-AES technology. This study therefore constitutes a strong basis for the interpretation of sedimentary records from the Chilean Fjords.