Majority of aquaculture practices are still based on extensive and semi-intensive farming systems though a trend to intensify operations to enhance yields and improve the efficiency of the production process has emerged in recent years. Apart from better management of water resources and water quality, use of high quality seed, optimising stocking densities of seed fish and refining feed and feeding techniques, usage of chemicals has contributed in increase in production efficiency as well as reduction of wastes and losses. Disease outbreak is a constant threat to the cultured stock that makes aquaculturists apply disease control chemicals to treat or prevent such outbreaks. A key problem however is a lack of sufficient knowledge and experience in use of chemicals that leads to their use or misuse. The chemicals used in intensive and sometimes in semi-intensive aquaculture typically include chemotherapeutants, feed additives, hormones, pesticides and parasiticides. Major environmental and human health issues associated with their use in aquaculture are discussed