In this project we present a study of the polluted water from two important water bodies in the Mexico-USA border: Lake Salton Sea (California) and Mexicali’s Lagoon (Baja California). We analyze the reaction of extremophile microorganisms (tardigrades) to pollution in order to evaluate its possible use as bioindicators of water quality. We have found that the resistance properties of tardigrades to extreme conditions become them excellent candidates to use them in polluted environment studies. Based on the tardigrades survival in the samples water, our results show that pollution is higher in Salton Sea than Mexicali’s Lagoon. Also we propose a nanotechnological solution for this problem using extremophiles unique capabilities.