To ensure that the customer of drinking water supply system (DWSS) at his water consumption point receives drinking water that meets all the biological, chemical, aesthetic and sanitary requirements is a challenge for water supply companies. It is difficult to maintain good water quality throughout the distribution network because there are numerous ways how drinking water might be contaminated. Causes of drinking water quality deterioration might be related to DWSS failures such as pipe breaks, corrosion of pipelines, bacterial regrowth, deteriorated water quality at water source, failure of drinking water purification station, etc., or to deliberate water contamination (Lee et al., 2012). It is not possible to predict type of contamination that may get into DWSS. It might be either biological or chemical, or even radioactive. However, on-line water quality monitoring systems could significantly reduce health risks related to water quality deterioration due to continuous data collection, automatic contamination detection and fast response to potential contamination. There are two main groups of on-line drinking water quality monitoring systems: 1) direct sensor system – a system that monitors concentration of a the specific compound directly; 2) surrogate sensor system – a system that monitors conventional water quality parameters that may be affected by a contamination event. Application of the direct sensor system provides precise concentration data for a target contaminant, but does not show overall drinking water quality. Meanwhile the surrogate sensor system shows the overall drinking water quality, but the contaminant itself and its concentration might remain unknown, since the correlation between measured data and actual contaminant concentrations are empirical (Che et al., 2014, Hall et al., 2007, Storey et al., 2011). Surrogate sensor systems have been intensively developed over the past few decades, and numerous experiments regarding correlation between contamination and conventional parameters of drinking water have been made. It was considered that surrogate sensor technology is the most promising. However, direct sensors and methods for biological contamination detection have been improved for on-line application during the last few years also. Therefore, a crucial choice has to be made between awareness of actual concentration of the most representative/hazardous contaminant and the possibility to detect more water quality variations caused by other agents. Respectively the direct or surrogate sensors have to be chosen. The goal of the current work is to highlight both systems advantages and limitations, and to identify the cases, where one or another system is more beneficial.