A dosing control system comprises a selective catalytic reduction (SCR) analysis module and a dosing management module. The SCR analysis module estimates ammonia (NH3) stored by an SCR catalyst, maximum NH3 storage capacity of the SCR catalyst, NH3 slip downstream of the SCR catalyst, NH3 oxidation, and NH3 conversion through reaction with nitrogen oxides (NOx). The NH3 stored is estimated based an amount of dosing agent injected, the NH3 slip, the NH3 oxidation, and the NH3 conversion. The dosing management module controls dosing agent injection into an exhaust system upstream of the SCR catalyst based on the NH3 stored by the SCR catalyst and the maximum NH3 storage capacity.