In an endeavor to tackle environmental problems, the photodegradation of microcystin-LR (MC-LR), one of the most common and toxic cyanotoxins, produced by the cyanobacteria blooms, was examined using nanostructured TiO2 photocatalysts (anatase, brookite, anatase–brookite, and C/N/S co-modified anatase–brookite) under UV-A, solar and visible light irradiation. The tailoring of TiO2 properties to hinder the electron–hole recombination and improve MC-LR adsorption on TiO2 surface was achieved by altering the preparation pH value. The highest photocatalytic efficiency was 97% and 99% with degradation rate of 0.002 mmol L−1 min−1 and 0.0007 mmol L−1 min−1 under UV and solar irradiation, respectively, using a bare TiO2 photocatalyst prepared at pH 10 with anatase to brookite ratio of ca. 1:2.5. However, the bare TiO2 samples were hardly active under visible light irradiation (25%) due to a large band gap. Upon UV, solar and vis irradiation, the complete MC-LR degradation (100%) was obtained in the presence of C/N/S co-modified TiO2 with a degradation rate constant of 0.26 min−1, 0.11 min−1 and 0.04 min−1, respectively. It was proposed that the remarkable activity of co-modified TiO2 might originate from its mixed-phase composition, mesoporous structure, and non-metal co-modification.