A system comprises a fuel system for delivering fuel to an engine for combustion and a reductant storage system for delivering reductant to the exhaust stream for an SCR catalyst for NOx reduction. The fuel system further comprises a water separator for separating water-based fluid from fuel in the fuel tank, and a separation reservoir to collect the separated water-based fluid. Based on readings of a water-in-fuel sensor positioned within the reservoir, a type of degradation (e.g., water build-up, high-water-content fuel, mis-filling of the reductant, etc.) may be determined and indicated.