The possible adverse effects of emerging contaminants (EC) on the environment and human health are currently one of the highest concerns in the scientific community and legislators. EC include a diverse array of compounds that have recently revealed to occur extensively in the environment and may induce a variety of potential toxic effects. This chapter describes the relevance of microscopy in the ecotoxicology field, in particular, in the study of the effects of some EC on aquatic organisms. Some representative examples are given to illustrate the application of microscopy in the detection of EC-induced lesions. Overall, microscopy coupled to other techniques is a valuable tool for ecotoxicology.