The invention relates to a system and method for detecting low quality reductant and catalyst degradation in selective catalytic reduction systems, in particular, a control system for a selective catalytic reduction (SCR) system includes a conversion efficiency determination module, an ammonia slip determination module, and a diagnostic module. The conversion efficiency determination module determines a conversion efficiency of an SCR catalyst. The ammonia slip determination module determines an amount of ammonia slip across the SCR catalyst when the conversion efficiency is less than a predetermined threshold. The diagnostic module determines pass/fail statuses of a reductant supply and the SCR catalyst based on the amount of ammonia slip and at least one ammonia slip threshold.