Sequencing batch reactors (SBRs) including aerobic SBRs and anaerobic SBRs (ASBRs) are partially emptied batch reactors that are widely used as bioprocesses in pollution control. We present dilution and biochemical materials balance modeling equations and simulation results for the partially emptied batch reactors, especially for ASBR treatment of low-strength wastewater. The simulated substrate and microbial concentrations for both dilution and materials balance equations follow the same pattern during both feeding and reaction times. However, the results of the materials balance equations show microbial activities during feeding as well as during reaction times and were found to be more appropriate for the biologic system in which substrate removal is associated with microbial growth. Furthermore, the simulation results point to the need to foster high microbial accumulation in the system during startup to optimize the process performance and the need to operate the system at a short reaction time, especially for low substrate concentrations. The results were found to be in agreement with the results of prior laboratory studies.