The Sontecomapan lagoon (Mexico) is a Ramsar site within the Los Tuxtlas Biosphere Reserve, facing the Gulf of Mexico. Although the site has a protected area status, it is vulnerable to microplastic contamination, whose long-term effects are uncertain. This study gives the first approach to the degree of contamination by microplastics in surface waters, zooplankton, and sediments in the lagoon. The samples in these three environmental compartments were collected in June 2018 and analyzed in the laboratory to extract and quantify the microplastics. The microplastics sampled were classified into fibers, fragments, and foams and identified as polyester, acrylic, and rayon, among others. In the surface waters, the mean concentration of microplastics was 7.5 ± 5.3 items/L, which is higher than the values registered in other protected coastal systems, perhaps because of differences in the methods used. Zooplankton, represented by copepods, luciferids, and chaetognaths, showed concentrations of 0.002 ± 0.005, 0.011 ± 0.011, and 0.019 ± 0.016 items/individual, respectively. These values were low compared to systems with high anthropic influence, and the differences between the three kinds of organisms were attributed to their feeding habits. In the sediments, the mean concentration was 8.5 ± 12.5 items/kg, lower than the values registered in sites of high human impact; the maximum value here found (43 items/kg) was recorded in the internal part of a lagoon arm of almost stagnant water. In general, the degree of contamination by microplastics in the lagoon was low; however, their presence indicates a potential risk to the biota.