Water quality monitoring of the distribution system is important in controlling the water quality in the system and also distributing the water to customer's taps. In the previous research, only the water quantity was considered as a factor of monitoring importance. Even if the water quality as well as the water quantity was considered, the retention times in the system was used to estimate the water quality at the network nodes. However the retention times cannot well represent the water quality because of their nonlinear relationship. In this paper, we present a new method of determining the optimal monitoring sites, in which the water quality is incorporated into the optimization model with a different method for water distribution system from the previous researches. In the method, the water quality at the nodes is determined by using a simulation model EPANET rather than retention times. In this paper, list processing algorithm is applied to track the shortest path of flow in a junction from water source. In the case of multi-water source system, network model is used for tracking the regional boundary of water distribution as followings; which source takes charge of a supply region, whether the source is changed by the pass of time or not, tracking of water source, the regional bounds by the amount of transmitted flow. So is applied to constructing the coverage matrix and determining all the flow paths. With the coverage matrix, an integer-programming problem is formulated and solved. Both the cases of steady-state and extended period simulations are analysed by the newly developed method. For the extended period simulation, minimal set of covering algorithm is used to locate the optimal monitoring sites. Our method provides more reasonable monitoring sites than those of the previous methods for two sample distribution networks.