Cyanotoxins have caused worldwide concern due to their diverse occurrence and toxic effects, which has led to an intensive search for cost-effective techniques for their removal from contaminated water. In this study, a novel biomaterial, protonated mesoporous graphitic carbon nitride (mpg-C3N4–H+) which is fabricated by treating mpg-C3N4 with concentrated hydrochloric acid, is applied as a promising bioadsorbent for the uptake of microcystins (MCs). The pH of the reaction media played a significant role in the removal of MCs; maximum adsorption occurred at pH 7. Kinetic studies showed that the adsorption of MC-LR and MC-RR onto the adsorbent was a rapid process. The mpgH+ exhibited high adsorption capacities of 2360.96 and 2868.78 μg g−1 from the Langmuir model for MC-LR/RR, respectively. The high adsorption capacity, good solvent stability, and excellent reusability make mpg-C3N4–H+ promising as a novel adsorbent for the adsorption and removal of MCs from aqueous solution. This information may be useful for further research and practical applications of the novel two-dimensional layered, mesoporous graphitic carbon nitride.