Bioindicator species are used in biomonitoring contaminant exposure. In order to evaluate how contamination exists spatially, sessile species are the best. In addition, a good bioindicator species is common and easily sampled, presenting some responses to toxicants (biomarker responses) that can be reliably measured and show concentration dependence. The suitability of bioindicator species varies markedly between aquatic bodies, as the sensitivities of organisms to different contaminants vary markedly. The commonly used model organisms are good bioindicator species only when they are common in the natural environment studied. Biomarkers of exposure indicate that the species has been exposed to a toxicant. Good examples are mRNAs, which show that exposure affects transcription, but do not give information on the effects of toxicants on the function of organisms. This is done by biomarkers of effect, which usually measure protein activities. The biomarker responses can be markedly affected by the presence of other compounds in the environment, by natural environmental stresses, and by the length of exposure. Effect–biomarker responses translate to ecosystem effects if the measured parameter affects the fitness of the organism studied.