Mercury (Hg) has been extensively studied due to its impact on the environment and health, but its effects on wild mammal populations are still poorly known. Therefore, the use of biomonitors has gained importance. Our objective was to report and compare, for the first time, the amount of mercury in small mammals belonging to three trophic guilds and to provide an initial toxicology perspective in the Mezquital Valley, a critically polluted area of Central Mexico. We quantified total Hg from the hair and liver of a nectarivorous bat (Leptonycteris yerbabuenae), an insectivorous bat (Corynorhinus townsendii) and a granivorous mouse (Peromyscus melanophrys) using atomic absorption spectrometry during the dry and rainy seasons. We compared the mercury concentrations between seasons, species and matrices. In all species, the average mercury content was higher in hair than liver, and there was no correlation between matrices. There was no difference in mercury content among species. Hg concentrations in the livers of P. melanophrys and C. townsendii were lower during the dry season than the rainy season, suggesting a seasonal decline in mercury availability. All of the values detected were below the neurotoxicity threshold reported in small mammals (10 ppm); however, we propose constant monitoring of Hg in their environment and confirm the utility of these species as biomonitors.