The versatility of the biological aerated filter (BAF) has made it an important process in wastewater treatment. These submerged three-phase fixed media reactors have been used in a wide variety of applications in wastewater treatment, such as primary treatment (solids removal), secondary treatment (COD and BOD removal), and tertiary treatment (nitrification). The aim of this work was to investigate the biological start-up of two such reactors to remove suspended solids (SS), total COD (tCOD) and ammonia, one containing a sunken medium (relative density 1.05) and the other containing a floating medium (relative density 0.92), both identical in shape and size. The reactors (0.054 m(3) media) were run in parallel in upflow mode using secondary effluent as the process liquid at a flowrate of 0.2 dm(3) min(-1) and air:liquid ratio of 10:1. Overall, floating media performed better than sunken media for SS, tCOD and ammonia removal, probably due to the compression of the bed due to the buoyancy force of the media and the flow of air and liquid acting upwards. Bed compression improved solids removal and appeared to have promoted the growth of bacteria. Temperature had a greater impact on nitrification than on carbonaceous matter removal. The floating medium reactor was more resistant to low temperature shocks than the sunken medium reactor but the latter showed a faster recovery time as temperature increased. Although the backwashing frequency used was satisfactory, performance may have improved if the backwashing had been carried out only when reactor performance began to decline. Nitrification was shown to follow a reaction rate between zero and half order. Thus, ammonia removal was generally independent of ammonia concentration and more affected by the presence of carbonaceous matter.