Occurrence and Toxigenic Potential of Planktonic Cyanobacterial Blooms and Benthic Mats in the Tropical Rio Grande de Comitán and Montebello Lakes National Park, Southern Mexico

The tropical aquatic ecosystems of the Río Grande de Comitán and Lagunas de Montebello National Park (southern Mexico) exhibit signs of advanced eutrophication, with environmental conditions that can promote the proliferation of potentially toxic cyanobacteria. This study assessed the distribution and ecotoxicological risk of planktonic blooms and benthic mats throughout the subbasin. Using a polyphasic approach combining cultured‐based analysis, molecular detection and HPLC, we found a low‐diversity cyanobacterial community dominated by Planktothrix agardhii , which reached densities up to 2.2 × 10 ⁵ cells/mL during the warmest months. Benthic Microcoleus sp. and localized blooms of Anabaenopsis elenkinii were documented. Molecular analyses confirmed the presence of microcystin and anatoxin synthesizing genes, with high microcystin concentrations detected (67.5–3169  μ g/L). Seasonal analyses revealed significant differences in temperature in both lakes (H = 20.8, p < 0.001) and rivers (H = 13.1, p = 0.0098), as well as in river K ₂₅ (H = 10.7, p = 0.0169). PCA explained 65% and 64% of the variance in the first two axes for lakes and rivers, respectively, separating sites according to gradients in nutrients, conductivity, and other water‐quality variables. In lakes, redundancy analysis (RDA) showed that the first two axes explained 72% of the constrained variation, with total nitrogen, specific conductance, total phosphorous, catchment disturbance index, pH, and dissolved oxygen contributing to the environmental gradients structuring cyanobacterial composition. Wastewater discharges from the upper basin (Comitán) act as a continuous source of nutrients and cyanobacterial inoculant, whereas tourism and fishing activities mechanically disperse these populations across the lakes. These results demonstrate the widespread occurrence of potentially toxic cyanobacteria across the subbasin and highlight the need for early‐warning and monitoring programs, particularly in areas affected by wastewater inputs and intensive human activities.