In situ continuous monitoring at high frequency is used to collect water quality information about water bodies. However, it is crucial that the collected data be evaluated and validated for the appropriate interpretation of the data so as to ensure that the monitoring programme is effective. Software tools for data quality assessment with a practical orientation are proposed. As water quality data often contain redundant information, multivariate methods can be used to detect correlations, pertinent information among variables and to identify multiple sensor faults. While principal component analysis can be used to reduce the dimensionality of the original variable data set, monitoring of some statistical metrics and their violation of confidence limits can be used to detect faulty or abnormal data and can help the user apply corrective action(s). The developed algorithms are illustrated with automated monitoring systems installed in an urban river and at the inlet of a wastewater treatment plant.