This disclosure describes wastewater treatment systems and methods of treating wastewater. In one exemplary method, a wastewater is split into first and second wastewater fractions. The first fraction is delivered to a membrane bioreactor, which may produce an effluent with a low pollutant concentration, and the second fraction is delivered to a biological wastewater treatment system, which may yield a higher pollution concentration yet have a shorter solids retention time. Some implementations of the invention can routinely meet or even exceed pollution discharge standards quite economically during normal operation, yet retain significant flexibility for handling seasonal or sudden variations in the flow rate of wastewater into the system. In select adaptations, waste activated sludge containing heterotrophs, autotrophs, and (optionally) polyphosphate accumulating organisms is delivered from the membrane bioreactor to the biological wastewater treatment system.