It is widely acknowledged that aquaculture represents the fastest growing food sector with an annual growth of approximately 10% [1]. Given the high growth rate of this sector, we must look to achieve a sustainable long-term production for the sake of the coming generations. Here we provide our opinion whereby we emphasize the need to rely and build on existing knowledge and studies, both social and environmental, as well as increasing state-of-the-art technologies on aquaculture practices. This will help to mitigate the potential impacts not only on the environment, but also on society at large, and will therefore ensure long-term sustainability. The aquaculture sector is a key industry providing a valuable food source to our increasing global population. Aquaculture, however, may also be a sector of activity which has significantly negative impacts on the environment, if not carried out in a sustainable way. One issue, for example, is the mass production of formulated feed which often contains natural fish products (fish meals and fish oils). The increasing demand for aquaculture feed (and other pet-feed) generates a high demand for fish, resulting sometimes in over-fishing of important fish stocks, thus indirectly affecting the overall sustainability of other marine resources [2].The industry is also regularly attributed to affect the natural environment drastically because of poor environmental practices. The excessive use of antibiotics, chemicals, and the intentional or unintentional destruction of important aquatic habitats such as mangroves, estuaries, and fjords; all important nursery grounds for wild fish stocks may also be generated if the industry develops without controls and regulations. Nevertheless, poor aquaculture practices may also affect nature besides the aquaculture industry itself by negatively altering aquatic resources through pollution of water bodies and sediments, inherently reducing the ecosystem carrying capacity. A number of notable negative events have occurred over the last decades that are associated with the aquaculture sector, most markedly the cases of widespread disease outbreaks. This has challenged the aquaculture sector everywhere across a range of farmed and wild organisms. Examples include infectious salmon anemia virus (ISAV), Acute Hepatopancreatic Necrosis Syndrome (AHPNS, also known as Early Mortality Syndrome or EMS) and regular Harmful Algae Blooms (HABs) occurring worldwide, generating fish and shellfish mass mortality or aquaculture products unfit for consumption [3,4]. Not only are such cases difficult for the farmers from an economical perspective (bankruptcy), but they also affect local communities which rely on the production and marketing of aquaculture products. This particular societal effect is even more important in areas where aquaculture is run as a “mom and pop business” and where cash flow is a crucial parameter that is not supported by international investments such as in large aquaculture farms. The disease control within the aquaculture industry, the social and environmental effects that are generated by aquaculture productions can be mitigated and managed by changing the industry’s habits from the initial planning stages through to the commercialization of aquaculture products. The solutions differ from one location to another, and are tied to the developmental stages of the sector in the various regions. The solution lies in the use of adapted legal framework which should be in line with social structures and environmental conditions, and the application of Best Aquaculture Technologies (BAT) such as state-of-the-art water treatment systems, water management tools, and means by which to firstly identify, then secondly to minimize and eliminate or mitigate disease occurrence and spread. Stakeholders such as government authorities, environmental companies, nature protection agencies, farmers and aquaculture associations, research institutes, not-for-profit companies, technology providers, and NGOs should ideally work together to ensure that such poor practices are an exception to the norm, and do not become the standard.