Many factors influence metal speciation in freshwaters. Metal species that are more soluble are considered more bioavailable and toxic. However, evaluation of metal speciation in waters is a complex task. Moreover, the quantification of total and dissolved metals is not suf- ficient to determine toxic effects on the biota. Here, we review environmental parameters that influence metal bioavailability: mathematical models to predict toxicity, and the biological tools used to evaluate contamination in freshwaters ecosystems. The major points are the following: (1) we discuss many ‘‘exceptions’’ of chemical parameters that are deemed to increase metal bioavailability or to protect against metal uptake, such as pH and water hardness. We provide evidence of organisms and environmental conditions that break these rules and therefore should be considered when predicting impairment by metals. (2) We discuss the advances in mathematical modelling as a proxy to metal toxicity. (3) We discuss advantages and limitations of using multiple biological tools to assess toxicity, such as the use of biomarkers and microorganisms, zooplankton, benthic macroinvertebrates and fish communities. Biomarkers are efficient in detecting low concentrations of metals in a short-term exposition. Changes on biological community structure and composition are good tools to detect high metal concentration or chronic concentration in a long-term exposition. The use of multiple tools including chemical analyses and a set of biological indicators is recommended for a more accurate evaluation of metal impacts on freshwater systems.