Nowadays, the term biomarker has become widespread in environmental sciences and ecology as shown by the increasing amount of research articles published on this topic in these research areas (2,042 articles published between 2000 and 2010 over a total of 2,352 published since 1985, WOK, ISI Web of Knowledge, http://www.isiknowledge.com). Despite this increasing enthusiasm for biomarkers, they are still poorly used in regulatory monitoring or ecological risk assessment. Indeed, the interest and pertinence of using biomarkers in such approaches have been questionned. While biomarkers of various toxicants for many species can be found in the literature, the limited extrapolation of biomarker results is particularly criticized and may prevent routine application. In this chapter, we discuss how to link biomarker responses to chemical exposure but also how to correlate them to effects at higher levels of biological organization. In the first part, the word biomarker is defined in the context of risk assessment. Then, the historical and current use of biomarkers in river biofilms, macroinvertebrates, and fish is shortly presented focusing on the specificity of biomarkers’ utilization in each of these biological entities. Next, laboratory and field studies are used to exemplify relationships between stressors and biomarkers but also between biomarkers at different levels of biological organization. Finally, current limitations of biomarkers are discussed and some propositions are made to overcome these limitations and to apply a multibiomarker approach to environmental risk assessment.