The paper defines the rational framework for understanding the mechanism of nitrogen removal in SBRs with multiple anoxic fill phases. Mass balance between denitrification potential and nitrate nitrogen introduced in each anoxic period sets the basis for optimal design. System evaluation shows that additional anoxic filling primarily avoids oversized reactor volumes as it reduces the internal recycle requirement. Low effluent nitrate levels can be achieved with dual anoxic systems with optimal hydraulic retention times. Higher denitrification potentials obtained by increasing the duration of the total anoxic period within the process phase (higher T-DN/T-P) can best be utilized by introducing multiple anoxic filling. Such systems may be optimized with an intermittent aeration continuous filling mode, which may be operated either with denitrification potential or available nitrate limitation. Model simulation of SBR behaviour also supports the results of optimal system design derived from process stoichiometry. (c) 2005 Elsevier Ltd. All rights reserved.