Abstract Production of pulp and paper from raw wood involves the washing of substantial quantities of highly coloured material from the wood pulp. Although most of this colour is trapped within the mill and the mills wastewater treatment system, discharge of coloured wastewater remains a problem of public concern. Lake Rotorua, New Zealand is filled with sediment consisting almost exclusively of diatoms. The most abundant species, Aulacoseira, has been shown to have very small pores, less than 200 nm, that could be very useful for the capture and holding of large organic molecules. Lake Rotorua is situated close to the two largest pulp and paper mills in New Zealand and may have to be dredged to solve a problem of eutrophication. Wastewaters generated at the Kinleith (Tokoroa) and Tasman (Kawerau) mills in the North island of New Zealand have been used to assess the characteristics of colour removal by Lake Rotorua diatoms. Vacuum filtration through the diatoms succeeded in removing colour but proved to be impractically slow as an industrial process. Addition of diatoms to wastewater streams in stirred experiments showed that significant adsorption took place. The majority of the colour was removed within 30 seconds of mixing. The efficiency of colour removal was found to vary between wastewater streams within the mills. The pH dependency of this removal was tested and found to be most effective in a pH range of 3.6 to 5. Attempts to reuse the diatoms showed that chemical backwash regimes were more effective than calcination. This study concluded that surface silanols were likely to be the principle agent in forming coagulants with the colour material and were subsequently trapped on the diatom surfaces, but more importantly within the pores.