The present work reviews the different biomarkers and organisms that have been used to assess pollution in aquatic ecosystems of Mexico in the last 16 years. Ninety-three publications were reviewed; they showed that 70 species, most of them native (70%), have been used for this purpose. Fish have been the most commonly used group, but other non-conventional organisms have also been used. Biomarkers of oxidative stress such as catalase and superoxide dismutase activity, as well as cellular lipid peroxidation, were the most widely used and versatile. Those used less frequently included Acetylcholinesterase, Ethoxyresorufin-Odeethylase or Metallothionein. The omic approach was used for Cytochrome P450, Vitellogenin and heat shock proteins. Sixty-two percent of the species were used only on one occasion during the period studied here, while 13% were used more than twice. Girardinichthys viviparrus and Goodea atripinnis were the most frequently used species due to their regional endemism, but their use was restricted to the center of the country. Forty-four percent of the studies evaluated the data from at least two weather stations, and only 10% of the studies monitored pollution levels during more than two seasonal cycles. In Mexico, traditional and omic biomarkers are commonly used by researchers; however, further investigation is needed to determine which species and biomarkers should be used for each region and particular situation. It requires a joint effort between research centers and public funding agencies for the development of regional and national monitoring networks.