Due to considerable losses in the agricultural sector, phytopathogenic viruses are of significant economic importance. Several phytopathogenic viruses have been detected in water bodies. These can be transmitted to their hosts through water contact. However, relatively few studies concentrate on the presence and impact of plant‐infecting viruses in water environments. In the present study, we used a metagenomic approach to determine viral phytopathogen diversity in wastewater, freshwater, and sludge from the southernmost tropical region in Mexico. We detected 15 different phytopathogenic viruses that belonged to the family Virgaviridae, genus Tobamovirus. Pepper mild mottle virus, tomato brown rugose fruit virus, and tropical soda apple mosaic virus had the highest number of reads. Phylogenetic analysis of the coat protein (CP) amino acid sequence revealed a close relationship between the solanaceous plant‐infecting viruses and the reference sequences found in GenBank. On the other hand, the CP amino acid sequence of Fabaceae and Cucurbitaceae‐infecting viruses did not show such a close relationship when compared with GenBank reference sequences. These results suggested that detected viral sequences could originate from new strains or species of local viruses likely from the consumption of locally cultivated produce, whereas those infecting solanaceous plants might come from consumption of processed or imported food to Mexico. The prevalence of a high diversity of plant viruses in wastewater and rivers and their potential infectivity raise concerns about the use of contaminated freshwater and wastewater in agriculture in Mexico.