Chile is the world’s leading exporter of farmed mussels, with an annual harvest of about 400,000 tonnes; this production is based on the capture of wild seeds, the availability of which may be threatened by climate change and overfishing. Climate change has led to a decrease in annual precipitation, which increases the salinity of the water column and may affect the vertical distribution of mussel populations in fjords. In Reloncaví Fjord, Chile, observed changes in precipitation are reducing freshwater inputs, leading to potential shifts in the habitat and distribution of the economically important Chilean mussel (Mytilus chilensis) and a competing species, Aulacomya atra. This study analyses the vertical dynamics of mussel beds in relation to changing environmental conditions, including freshwater inputs, salinity and hydrological regimes in a fjord exploited for mussel seed collection. The results suggest that decreasing trends in precipitation could lead to increased surface salinity, reducing M. chilensis beds while favouring A. atra, with negative consequences for wild seed collection, thus threatening the Chilean mussel farming industry and predicting socio-economic consequences for small-scale aquaculture. This study also describes the increasing fishing pressure on wild mussel larvae, suggesting joint effects that cannot be disentangled with the information currently available and that represent a key challenge for the design of adaptation measures to climate change. Therefore, this study highlights the need for better monitoring of mussel beds together with seed production and oceanographic conditions, as well as improving aquaculture practices that reduce unnecessary pressure on mussel beds through seed collection in the face of changing environmental conditions.