The data presented correspond to the number of microplastic particles in a liter of water collected in the Sontecomapan lagoon, Mexico. Sampling was done in June 2018 and October 2019 in 10/12 sites of the lagoon and the collecting method consisted of obtaining surface water with a 10-liter container; the content was stirred manually, and then, one liter of water was transferred to a 1-liter glass flask and kept at 4 °C. In the laboratory, the water was sieved through two coupled sieves (4.75 and 0.053 mm), and the retained material between the sieves was subjected to organic matter oxidation with hydrogen peroxide. Microplastic detection was made using a Raman DXR microscope Thermo Fisher, and the concentration of microplastics was expressed as the number of particles per liter of water. In June, microplastic particles were found in all the ten sampling stations examined, in a range of 7 to 26 part/L (mean concentration 13.5 part/L). In October, twelve samples were taken, but five were broken during the transport; in this month, concentration varied between 0 and 6 part/L (mean concentration 2 part/L).