A plant-integrated measurement and monitoring system includes one or more sampling ports disposed throughout to provide fuel samples at key locations in the plant. Additional sampling ports are included to provide samples of water, lube oil or other fluids. Each fuel sample is analyzed in an automated analyzer that determines a presence of contaminants. Results of the analysis are interpreted by the plant control system to determine quality attributes of the fuel samples and identify locations and/or causes of identified anomalies. The control system further issues alerts or actions to limit an impact of the identified anomalies.