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There is a long history of regulating chemical compounds in the aquatic environment. In the current context, environmental quality standards under the Water Framework Directive provide a useful model for monitoring concentrations of antibiotics in water, while monitoring fecal indicators under the Bathing Water Directive provides one for microbiological pollution.

Environmental quality standards set a concentration of a particular chemical that should not be exceeded in a water body. The standard is set based on the toxicity to the most sensitive species in a range from algae, through invertebrates, to fish and predators like otters, birds or humans. The toxicity assessment considers the predicted no effect concentration (PNEC) i.e. that at which no adverse effects are expected. It is similar in concept to the MSC used in microbiology, though the MSC is the lowest concentration at which selection pressure may occur.

Setting environmental quality standards for antibiotics is difficult, because currently there is limited toxicity information available. A PNEC is only available for about 20 out of a total 111 antibiotics, and for a very limited range of species. Setting quality standards without information for an adequate range of organisms can lead to conservative risk factors, which may produce very challenging standards with limited supporting evidence.