In Chile, coastal shellfish aquaculture activities are focused on bivalves, such as oysters, mussels, and scallops, and gastropods, such as abalone. From 1990, shellfish aquaculture has experienced an annual average growth rate of ~18%. Shellfish farming accounted with ca. 80,000 tons, or 14 % of total biomass and Chile is the third and second largest producer of scallops and mussels in the world, respectively. Although the industry has thrived in the past decade, global drivers such as climate and market variability and anthropogenic activities provide major challenges in sustaining the future of the aquaculture sector in our coastal ocean. The Chilean mussel farming industry is currently going through a severe crisis. Reasons are multiple and include the global financial crisis, interactions with several anthropogenic impacts and production targets, which exceed ecosystems caring capacities. Most importantly, low seed production has been detected, which seems to be associated with changes in the chemical characteristics of coastal waters associated to global (e.g. climate change effects) and local anthropogenic stressors (e.g. pollutants and eutrophication). Furthermore, the Chilean scallop farming industry in northern Chile has been regularly affected by large events of larval mortality, potentially driven by the effect of corrosive upwelling waters. Similar events have been reported in Oregon and Washington (USA), with potentially devastating effects on their industry, which generates nearly $300 million dollars annually for the coastal economy.