Constantly we have to deal with an exponential increase in the amount of different chemical compounds that industries synthesize and manufacture, such as drugs, pesticides, persistent organic pollutants, preservatives, and personal hygiene products. Many of these chemical substances are biologically active and interact with biomolecules, such as proteins, through specific mechanisms that lead to different biological responses. Due to the inherent risk of many compounds to the environment and to humans, their toxicological activities must be evaluated. In order to evaluate the biological activity of molecules, three types of experiments can be used: in vivo (e.g., animal tests); in vitro (e.g., cell tissue culture); and in silico simulations. In vivo and in vitro experiments are time-consuming and expensive processes, in addition to causing ethical discussions and debates. An alternative to avoid these setbacks is the use of in silico models. The scientific community thus begins to use in silico models as a possible alternative, developing a large number of models and strategies capable of predicting the toxicological properties of several chemical compounds. This review discusses methods that employ in silico models to assess and predict the possible effects of contaminants found in natural waters. manufacture drugs pesticides pollutants preservatives products biomolecules proteins responses humans evaluated molecules used e.g., eg e g (e.g. tests tests) culture culture) simulations timeconsuming time consuming processes debates waters e.g. (e.g e.g