We investigated the relative distribution of allochthonous (i.e., terrigenous) organic matter in the complex, continuous, river–fjord–sound–channel–gulf system of Chile’s North Patagonia (41.5–46.5°S) in order to establish whether this organic matter can reach the open ocean or whether it is largely retained near its fluvial sources. Grain size distribution, total organic carbon and total nitrogen contents, and carbon stable isotope contents (δ13C) were quantified in 53 surface sediment samples collected during the CIMAR Fiordos cruises 1, 4, 8, and 10, as were salinity and silicic acid concentrations in the surface waters. A principal component analysis segregated the Chiloé and Aysén interior seas into two zones: (i) the continental fjords, with sediment enriched in allochthonous organic matter, having higher C:N molar ratios (10–14) and lower δ13C composition (−23‰ to −27‰); and (ii) the channels and gulfs, with a prevalent autochthonous marine source, having lower C:N values (6–10) and higher δ13C composition (−20‰ to −23‰). Estuarine waters with low salinity (2–30) and high silicic acid (10–90 μM) were associated with high C:N ratios and low δ13C in surface sediments, meaning that terrestrial organic matter was transported up to the mouth of the continental fjords. A two-source mixing model confirmed that allochthonous (terrestrial) organic matter contents (50–90%) associated with local river discharges were present within the continental fjords. On the contrary, autochthonous (marine) organic matter was prevalent (50–90%) at the sites in the marine influenced channels, sounds, and gulfs.