Photocatalysis has been shown to successfully remove microcystins (MC) in laboratory experiments. Most research to date has been performed under ideal conditions in pure or ultrapure water. In this investigation the efficiency of photocatalysis using titanium dioxide was examined in a complex matrix (waste stabilisation lagoon water). A flow-through photocatalytic reactor was used for the photocatalytic removal of four commonly-occurring microcystin analogues (MC-YR, MC-RR, MC-LR, and MC-LA). Up to 51% removal for single MC analogues in waste lagoon water was observed. Similar removal rates were observed when a mixture of all four MC analogues was treated. Although treatment of MC-containing cyanobacterial cells of Microcystis aeruginosa resulted in no decline in cell numbers, or viability with the current reactor design and treatment regime, the photocatalytic treatment did improve the overall quality of waste lagoon water. This study demonstrates that, despite the presence of natural organic matter, the microcystins could be successfully degraded in a complex environmental matrix.