The monitoring of biological effects has recently become an integral component of environmental monitoring programmes as a supplement to the commonly used contaminant monitoring. Over the years, many biomarkers have been developed that are claimed to be efficient at providing an early warning of deleterious effects on biological systems and for estimating biological effects due to contaminants. Although biomarkers are potentially useful, they have a number of important limitations. In this paper, we examine some of the key assumptions behind the theory and practice of use of biomarkers, and propose a scheme, which may facilitate decisions by environmental managers as to how and when to use biomarkers in their monitoring programmes.