Display omitted •A g-C3N4/TiO2 floating photocatalyst was prepared via a facile sol-gel method.•M. aeruginosa and Microcystin-LR were simultaneously removed under visible light.•Photoinduced holes and OH are the reactive species involved in photocatalysis.•Microcystin-LR was gradually degraded with oxidation of the Adda chain occurring.•The floating photocatalyst can be readily recovered for reuse. Harmful algal blooms (HABs) have increasingly occurred worldwide causing human and ecological health risks. In this study, we report on an effective alternative to inactivating Microcystis aeruginosa under visible light irradiation with the use of a floating heterojunction photocatalyst. The photocatalyst (CTAE for short) is made of graphitic carbon nitride (g-C3N4) and TiO2 that are loaded on Al2O3-modified expanded perlite via a facile sol-gel method. The N/C doping in TiO2 and the interaction between TiO2 and g-C3N4 enhanced the generation of h+ and OH independent of O2 activation, which could facilitate applications in oxygen-deficient waters. Consideration was given to the impacts of different mass ratios of g-C3N4 to TiO2. The photocatalysts were characterized by XRD, N2 adsorption/desorption isotherms, FESEM/EDS, TEM, XPS, UV–vis absorption and Photoluminescence spectroscopy. Results showed that different contents of g-C3N4 had an influence on the crystal structure, specific surface area and pore volumes of the photocatalysts. The use of 2 g/L of 0.03CTAE (i.e., the theoretical mass ratio of g-C3N4 to TiO2 = 0.03) photocatalyst could simultaneously remove 88.1% of M. aeruginosa at an initial concentration of 2.7 × 106 cells/mL and 54.4% of Microcystin-LR at an initial concentration of 50 μg/L following 6-h of visible light irradiation. Microcystin-LR was gradually degraded with oxidation of the Adda chain occurring. Following each treatment, the floating g-C3N4/TiO2 photocatalyst could be readily recovered from the solution, demonstrating a great potential for in situ remediation of eutrophic waters.