Ultraviolet light-emitting diodes (UV-LED) can be a good option for disinfecting water in small and decentralized facilities. A flow-through UV-LED disinfection module was evaluated at three remote locations in Japan. The disinfection efficiency of the module was monitored for over one year, targeting indigenous Escherichia coli, total coliforms, standard plate count, and heterotrophic plate count (HPC) bacteria. The physicochemical parameters of the source water, including UV transmittance (UVT), were also monitored to understand their natural fluctuation and impacts on UV disinfection. Overall, the UV-LED module showed efficient disinfection at all locations, achieving 2.7 log inactivation of E. coli at 30 L/min in a community-based water supply. HPC inactivation did not significantly differ among the three test sites (p > 0.01). One test site experienced a decrease in HPC inactivation after 10 months, whereas the other two sites did not show performance deterioration after one year. HPC inactivation was not correlated with the UVT of source water at any location, implying the difficulty to use UVT as a single parameter to predict disinfection efficiency in practical applications. This study demonstrates the effectiveness of UV-LED technology for water disinfection in small and decentralized water supply systems.