Aquaculture is the fastest growing animal food production sector worldwide and is becoming the main source of aquatic animal foodstuff for human consumption. However, the aquaculture sector has been strongly criticized for its environmental impacts. It can cause discharge and accumulation of residual nutrients in the areas surrounding the production farms. This is because, of the total nutrients supplied to production ponds, only 30% are converted into product, while the rest is usually discharged into the environment to maintain water quality in aquaculture culture systems, thereby altering the physic-chemical characteristics of the receiving water. In contrast, this same accumulation of nutrients is gaining importance within the agricultural sector, as it has been reported that the main nutrients required by plants for their development are found in this aquaculture waste. The purpose of this review article is to indicate the different aquaculture production systems, the waste they generate, as well as the negative effects of their discharge into the environment. Biofiltration and bioremediation processes are mentioned as alternatives for aquaculture waste management. Furthermore, the state of the art in the treatment and utilization of aquaculture waste as a mineral source for agricultural nutrition through biodigestion and biomineralization processes is described. Finally, aquaponics is referred to as a biological production approach that, through efficient use of water and recycling of accumulated organic nutrients in aquaculture systems, can contribute to addressing the goals of sustainable aquaculture development.