The culture of aquatic plants and animals for the use of mankind involves varying degrees of interaction between the organism being cultured and its physical and biological environment. This review of the current literature on aquaculture and the physical and biological environment is divided into two main subjects. The first is the way in which aquaculture directly affects the environment through the output or consumption of materials. The second is how aquaculture can affect the environment indirectly, particularly the biological community. Both the positive and negative aspects of potential and real impacts are examined in finfish, shellfish, and plant culture. Within each of the specific topics, mitigation of negative effects is discussed. No simple set of rules can be used to generalize the effect of aquaculture. The interactions between aquaculture practice and the environment is very specific to each combination of production and the biological and physical makeup of the location.