The taxonomic richness, composition, abundance, and biomass of pelagic microcrustaceans (Cladocera and Copepoda) were determined in 17 lakes of the “Lagunas de Montebello” National Park, a karst lake district in Chiapas State, southeast Mexico. The selected aquatic bodies exemplify the lake diversity in the area, which displays an anthropic impact gradient from impacted/eutrophic lakes on the NW to non-impacted/oligotrophic lakes on the SE. Sampling was conducted in two contrasting climatic periods: warm-rainy and cold-dry seasons. There were 32 taxa, five calanoid copepods, 16 cyclopoid copepods, and 11 cladocerans. The highest taxonomic richness, abundance, and biomass were found in the impacted/eutrophic lakes and the lowest in the non-impacted/oligotrophic lakes. Nauplii and copepods were the most abundant, while the copepods provided the largest biomass. Small-sized individuals composed the most significant abundance and biomass in impacted/eutrophic lakes, while large-sized individuals in the non-impacted/oligotrophic lakes. Even though the studied lakes belong to the same lake district, they showed low taxonomic similarity. Not a single taxon was found in all lakes; the most distributed taxa (13–14 lakes) were Mastigodiaptomus nesus and Leptodiaptomus cuauhtemoci, while 15 taxa (47%) were found in only 1–3 lakes. This karst lake district showed a great regional microcrustacean taxonomic richness but a great singularity level in each lake.