Aquaculture is developing and growing at the fastest rate compared to other food production systems (e.g. chicken and pig production). In this context, Chile has also increased its production in the past decade, with different salmonid species and mussel as their main products. However, during the past 20 to 30 years the awareness of the environmental impacts of these activities has produced an increment in regulations, development of certification bodies, among others, making these food-systems more complex, but also a more sustainable activity. Nevertheless, as aquaculture develops new environmental threats emerge. For example, right now it is possible to recognize environmental impacts near aquaculture farms e.g., organic sedimentation under the culture cages, but also far-farm environmental consequences that are much less understood. Antibiotics for example have been found several kilometers away of the nearest aquaculture facility in southern Chile. Another example is related to the diet modifications (alternative ingredients replacing fish meal and oils) that have been introduced as one of the main advances for finfish production, especially for salmon aquaculture. But on the other hand, finfish aquaculture is currently facing other environmental conflicts such as impacts such as water and soil degradation in terrestrial agriculture systems. This contribution presents the actual situation of aquaculture in Chile towards the development of a renewed regulation framework that should assure higher sustainability standards, facing challenges such those imposed by climate change driven events.