A controller for controlling operation of an aftertreatment system that is configured to treat constituents of an exhaust gas produced by an engine, the aftertreatment system including a selective catalytic reduction (SCR) catalyst, the controller configured to: generate a short-term cumulative degradation estimate of the SCR catalyst corresponding to reversible degradation of the SCR catalyst due to sulfur and/or hydrocarbons based on a SCR catalyst temperature parameter; generate a long-term cumulative degradation estimate of the SCR catalyst corresponding to thermal aging of the SCR catalyst based on the SCR catalyst temperature parameter; generate a combined degradation estimate of the SCR catalyst based on the short-term cumulative degradation estimate and the long-term cumulative degradation estimate; and adjust an amount of reductant and/or an amount of hydrocarbons inserted into the aftertreatment system based on the combined degradation estimate of the SCR catalyst.