Given its geographic characteristics, the southern Chilean fjord area is subjected to growing environmental pressure from the development of diverse forms of aquaculture (i.e., fish, algae, shellfish). The sediments accumulate substances as a natural sink, and ecotoxicology assays offer a reliable and robust proxy for sediment quality analyses. This study's objective was to establish a mid-range toxicity base line for the sediments in the region by applying a battery of non-specific ecotoxicological assays. Sediment samples (28) were collected in the channels and fjords studied during the CIMAR-Fiordos 11 cruise (July 2005). The sediments were evaluated using different species endemic to the eastern Pacific as targets: Ampelisca araucana, Tisbe longicornis, Arbacia spatuligera, and Dunaliella tertiolecta. The conditions for each assay were reported previously. Of the four species used as ecotoxicological tools, only D. tertiolecta differed significantly from the control group (negative) in terms of its growth. This difference could be attributed to nutrient enrichment. In general, we concluded that, although local changes occurred in the sediments, the mesoscale magnitude of the ecotoxicological alterations was small. Nonetheless, a surveillance program should be implemented that would allow us to follow-up and analyze the changes that are taking place in the systems on broader scales of time and space.