As recognition of the importance of aquaculture as a major protein source for human nutrition is growing, the issue of antibiotic residues in cultured fish and shrimp is increasing as well. To reduce potential disease risks, fish farmers often use antimicrobial agents during production. Misuse, overuse and improper withdrawal periods of antimicrobials could result in harvested products containing certain chemicals above the established maximum residue levels (MRL). As these products pose a health risk to consumer, they are not allowed on the market. This leads to disposal of product, therefore contributing to food loss and waste (FLW), as well as a loss in economic value to the producer.

Fish can be harvested from waters that are contaminated by varying amounts of industrial chemicals, including heavy metals and pesticides. These contaminants may accumulate in fish at levels that can cause human health problems (e.g., carcinogenic and mutagenic effects). The hazard is most commonly associated with exposure over a prolonged period of time (chronic exposure). Illnesses related to a single exposure (one meal) are very rare. Concern for these contaminants primarily focuses on fish harvested from aquaculture ponds, freshwater bodies, estuaries, and near-shore coastal waters (e.g., areas subject to shoreside contaminant discharges), rather than from the open ocean. Environmental chemicals and pesticides may also accumulate in aquacultured fish through contaminated feed ingredients (e.g., pesticides in oil-containing feed ingredients derived from near-shore bait fish). 

Other major concerns which cause food safety concerns and market rejection include environmental chemical contaminants, food safety and traceability. For example, pesticide residues can still be found in cultivated fish. Pesticides may come from underground water sources used for aquaculture. Aquaculture feeds have also been linked to the concentration of contaminants such as dioxin in certain farmed fish.  

In the case of aquaculture, the primary potential chemical hazards of concern include intentionally added chemicals such as veterinary drugs used in aquaculture production and unintentional contaminants such as persistent environmental contaminants that might be present in the production areas. In addition, certain types of marine fish naturally contain toxic compounds or may be particularly susceptible to contamination with naturally-occurring toxins, although they generally are not hazards of concern in the predominant species used in aquaculture.

Information on the permitted levels or maximum residue levels (MRL) of various veterinary drugs and other substances are provided by the Codex Alimentarius Commission.