An emissions control system is disclosed. The emissions control system may have a power source that creates a flow of exhaust, an SCR catalyst situated to receive the flow of exhaust, and an injector configured to inject a reduction agent into the flow of exhaust in the presence of the SCR catalyst. The emissions control system may further have a controller configured to calculate a spatially dependent surface coverage of the reduction agent on the SCR catalyst and substantially stop injection of the reduction agent when the spatially dependent surface coverage of the reduction agent exceeds a maximum surface coverage of the reduction agent at one or more spatial locations.