Human activities have led to an increased influx of carbon into lakes due to changes in land use that result in higher erosion rates, eutrophication, and the introduction of organic matter. This, in turn, causes greater carbon exports and carbon accumulation in sediments. In our study, we estimated the fluxes of total particulate carbon (FTPC), particulate organic carbon (FPOC), and particulate inorganic carbon (FPIC) in three lakes with different trophic statuses. Two lakes, one eutrophic (Bosque Azul) and one mesotrophic (San José), are in the anthropically impacted zone of the plateau. In contrast, an oligotrophic lake (Tziscao) is in the mountainous, pristine area of “Lagunas de Montebello” National Park, a tropical karst lake district in Chiapas, Mexico. Our findings revealed that the highest FPOC values were observed in the eutrophic lake (0.47 ± 0.2 g m−2 d−1), while the highest FPIC were observed in the mesotrophic lake (1.11 ± 0.8 g m−2 d−1). In contrast, the oligotrophic lake exhibited the lowest fluxes. Eutrophication increased the levels of FPOC, while deforestation and erosion contributed to the rise in FPIC. Eutrophication and erosion in the lakes of LMNP led to five-, two-, and sixteen-fold increases in the FTPC, FPOC, and FPIC, respectively.