Managing waste nutrients from intensive freshwater and marine pond aquaculture is a global challenge. Nutrient-enriched water released from farms can have detrimental effects on aquatic ecosystem health. There are a range of treatment options for discharge water from fish and crustacean ponds, and this review examines the benefits and limitations of these options. Much of the nutrient waste is derived from the addition of formulated feed. In recent years, reduction in waste from feeds and feeding has been largely incremental. In terms of treatment, there are low-cost approaches, such as settlement ponds, but they are inefficient at reducing nutrients. Biological systems, using aquatic plants, microalgae and filter feeders to reduce nutrient release from farms have variable levels of effectiveness. Establishing wetlands requires considerable additional land area, and success to date has been highly variable. Overall, this review found no simple cost-effective solution for managing nutrient enriched water from ponds. This is due, in many cases, to challenges with treating the large volumes of discharge water with relatively low nutrient concentrations. This means that more technologically advanced and reliable treatment options, for example, bioreactors, are prohibitively expensive. However, some systems, such as use of recirculation systems typically increase nutrient concentrations, and hence the efficiency and effectiveness of more expensive treatment methods. Biofloc systems can also provide a mechanism for in-situ nutrient treatment as well as a supplementary food source for animals. Overall, there is scope to improve treatment of waste nutrients, but significant modifications to many production systems are needed to achieve this.