The effect of surface topography on the long-term development (≈10 weeks) of biofilms has been investigated using a monitoring technique based on images produced by a flat-bed scanner and initially developed for flat surfaces. The biofilm response to rotation speed changes in lab-scale rotating biological contactors (RBCs) has been studied. Two RBCs, each containing five discs (two with flat surfaces and three with rough surfaces) were run initially at two different rotation speeds: 4 rpm for reactor I and 40 rpm for reactor II. After 47 days, the rotation speed was increased in reactor I to 40 rpm and decreased in reactor II to 4 rpm. Prior to the rotation speed change, the biofilm on the flat discs underwent large detachments in both reactors, but the biofilm on rough discs was less extensively damaged. The increase in rotation speed induced large detachments of the biofilm in reactor I on all discs, but the biofilm on the rough discs recovered more effectively with faster regrowth. In reactor II, the decrease in rotation speed favored the development of the biofilm. Wall stress distributions obtained from CFD simulations on flat and rough discs at different rotation speeds were well correlated with experimental observations.