A biofilm process with the attached bacterial growth onto ceramic media was applied to remove carbonaceous and nitrogenous pollutants from nonpoint water source. The packing ratios of ceramic media were 0.05 and 0.15 (v/v). Thereafter, the reactors were operated intermittently in sequencing batch mode with different cycle periods: 0, 5, 10 and 15 d. The COD and NH4+-N removal efficiencies were investigated under different operating conditions, such as media packing ratio, temperature and interevent period. Additionally, polymerase chain reaction (PCR)-denaturing gel gradient electrophoresis (DGGE) and INT-dehydrogenase activity (DHA) tests were conducted to observe the microbial community and activity in the biofilm. Consequently, the removal efficiency of the organic matter after 8 h remained stable, even with longer interevent periods, regardless of the packing ratio. The interevent period and packing ratio seemed to have no significant influence on the COD removal efficiency. However, stable nitrification efficiency, with longer interevent period, was only achieved with a packing ratio of 0.15. Therefore, a packing ratio above 0.15 was required to simultaneously achieve stable COD removal and nitrification efficiency. The DGGE profiles revealed that the prevalent microorganism species were changed from that of the seeded activated sludge into those detected in the sediments. Due to the prevalence of microorganisms related to the sediment, their activities did not decrease, even after a 15 d interevent period.