A method and system for mitigating a urea deposit within an SCR system that includes determining a mass of an accumulated urea deposit present within the SCR catalyst and SCR piping, comparing the mass of the accumulated urea deposit with a deposit upper threshold limit, and initiating an SCR regeneration event when the mass of the accumulated urea deposit is greater than the deposit upper threshold limit. The method further includes determining an amount of NH3 passing through the SCR catalyst downstream of the urea deposit, comparing the amount of NH3 passing through the SCR catalyst with an NH3 regeneration threshold limit, and terminating the SCR regeneration event when the level of NH3 passing through the SCR catalyst is less than the SCR NH3 regeneration threshold.