The AZTI’s marine biotic index (AMBI), an ecological indicator for managing estuarine and coastal waters worldwide, was tested in two fjords in Chilean Patagonia. The Aysen Fjord (42° Lat. S) supports intensive salmon farming in coastal ecosystems, while the Baker Fjord (48° Lat. S) is currently just beyond the limit of the southern expansion of salmon concessions. The ecological status of the Aysen Fjord was classified as good, while the status of the Baker Fjord was classified as high and unbalanced. These differences were consistent with our expectations, illustrating the effect of local environmental conditions and human activities, combined with river inputs into semi-confined fjords. This method is appropriate for the evaluation of the ecological status of the fjords, but requires a sufficient amount of data for the robust environmental assessment as proposed by the Water Framework Directive (WFD).