Salmon farming in southern Chile occurs in fjords and channels with marked environmental heterogeneity, which can influence benthic response to salmon farming pressure and consequently regulatory compliance. This study aims to identify patterns associated with environmental variables on soft bottom areas exposed to salmon farming and their relationships with the prevalence of anaerobic sediments in Aysén and Magallanes regions. Historical monitoring data from Sernapesca (2012–2023) were analyzed, classifying farms by substrate type (soft, hard, mixed) and qualification status (aerobic and anaerobic), and evaluating relationships with environmental variables and their influence on benthic macrofauna richness and abundance.
Soft-bottom farms represented ~20% of active sites over the last decade. In Aysén, the proportion of sites exhibiting anaerobiosis reached 40% for soft-bottom areas and 29% for hard-bottom areas, and 80% and 26%, respectively, in Magallanes. Principal Component Analysis of sediment and water column variables revealed distinct regional separation (Figure 1). The PCA structure reflected: (i) an estuarine–marine gradient (salinity, temperature, mud content; PC1), (ii) a gradient describing benthic oxygenation conditions (redox potential, organic matter; PC2), and (iii) a gradient potentially linked to physicochemical processes associated with bottom depth and pH (PC3) (Figure 1).
These findings indicate that site-specific environmental baselines are essential for regulation, either to assig areas for salmon farming sites, as well as to establish thresholds, since uniform ones may fail to account for regional differences in substrate and ecosystem dynamics. Adaptive frameworks integrating local variability could improve environmental sustainability and guide the spatial planning of salmon farming, particularly in sensitive soft-bottom habitats where current practices may exacerbate benthic degradation.