Fractal dimension was used to describe morphology of a biofilm. Images of biofilm sections were obtained with a confocal laser scanning microscope and were further enhanced using image analysis software. Fractal dimensions were estimated from the slopes of cross-correlation functions. Two geometric scales with different fractal dimensions were identified in the biofilm. Small scale biomass clusters (< 5 μm) had fractal dimensions close to the topological dimension while the fractal dimensions of larger aggregates were considerably smaller. Anisotropic morphology was also detected by the difference of fractal dimensions and was possibly related to the direction of water flow.