The southernmost Patagonian region constitutes a major glaciered area with a high freshwater input loaded with particulate and dissolved matter. We assessed the relevance of the terrestrial (allochthonous) and marine (autochthonous) matter that permeates into the fjord and channel system and their possible impact on the euphausiid-based food web. A research cruise (CIMAR 16) was conducted from 18 October to 13 November 2010 (austral spring) in the area between Magellan Strait and Drake Passage to study the physical-chemical and biological characteristics of the pelagic food web, as well as the main biological processes linked with the food web. The dominance of phytoplankton within the autochthonous fractions of particulate organic carbon (POC) and the high abundance and bacterivory rate shown by the heterotrophic nanoflagellates suggest an interplay between microbial and classical food webs. Euphausia vallentini showed a moderate grazing impact (3% of the gross primary production) and a daily ration of 18.6%, and the fecal pellet production rate corresponded to 24.5% of the ingestion rate. This species removed heterotrophic prey (67.5%) preferentially over diatoms (32.5%), and the ingested diet was mainly dinoflagellates, tintinnids, crustacean nauplii and centric diatoms. Overall, euphausiids fed preferentially on marine matter, which showed a tight link with the pelagic food web. Congeneric species of the genus Euphausia shared the condition of 'key species' as they constitute a major carbon and energy flow from lower to higher trophic levels and an important part of the POC flux through their active vertical migration and passive fecal-carbon export.