Mexican aquaculture production systems have been analyzed here in areas of the Pacific, Gulf of Mexico, and the Caribbean Sea. The species that are developed in aquaculture systems are: oysters (Crassostrea gigas, Crassostrea corteziensis), abalone (Haliotis fulgens, Haliotis rufescens), clams (Panopea generosa), shrimp (Litopenaeus vannamei), prawn (Macrobachium rosenbergii), tuna (Thunnus thynnus), tilapia (Oreochromis niloticus), carp (Cyprinus carpio), trout (Oncorhynchus mykiss), catfish (Ictalurus punctatus), and bass (Micropterus salmoides). There are also other species, obtained by fisheries, used to develop aquaculture production systems. From the total aquaculture production units (APU) in the southern Gulf of Mexico, 62% were identified as units engaged in tilapia culture and 38% in fattening and breeding. This is a risk and may increase the impact on aquatic ecosystems by effluents generated by these aquaculture activities. These effluents contain different components, among which are organic matter, nitrogen, and phosphorus. There are different studies for the treatment of these effluents, but are little applied to real scale, as they are performed at laboratory level. It is required to apply and obtain functional technology for producers of aquaculture systems in order to avoid the impact to ecosystems and also keep these chemical and biological hazards away from aquatic environments.