BACKGROUND: Textile dyes are hardly removed from effluents by conventional wastewater treatment but can be degraded by a number of physicochemical processes, which nevertheless have specific limitations. The development of bioremediation processes may provide a viable alternative. RESULTS: Resting cells of three aquatic fungal strains, Alternaria sp. (Tt-S1), Coniothyrium sp. (Kl-S5) and Phoma sp. (DSM22425), were evaluated for their ability to decolorize model effluents of different dye application classes. Phoma sp., which decolorized all four applied model wastewaters (MWW), was immobilized on a polyester-based fleece material originally designed for use as cooker-hood filters, and applied in internal loop airlift and bubble column reactors in repeated batch mode under sterile and non-sterile conditions. Depending on the applied MWW and bioreactor setup, a decolorization of more than 90% was achieved in three consecutive treatment cycles and total operating time of 16 days. In an upscaled reactor (10 L), Phoma sp. decolorized MWW containing acid dyes by 61%. Chemical oxygen demand of the MWW was reduced by 36%. CONCLUSION: The results presented underline the potential of aquatic fungi for the development of textile dyeing effluent treatment processes. Copyright (c) 2012 Society of Chemical Industry