The liver fluke Opisthorchis viverrini s.l. is associated with a long-term public health problem in Thailand. However, O. viverrini s.l. infection in Bithynia snails in the canal network system (CNS) in the Bangkok Metropolitan Region (BMR) has never been assessed. This study aimed to investigate the occurrence of B. siamensis siamensis and the prevalence of O. viverrini s.l. infection in this snail in the CNS in BMR along with morphological examination and molecular analyses on O. viverrini s.l. cercariae. The snails were randomly sampled from the CNS in all BMR areas from January 2018 to July 2019. Snail specimens were identified and examined for digenean infection by shedding and dissection. The cercariae were identified using morphology and molecular methods, including PCR with a species-specific primer and a Bayesian phylogenetic analysis of ITS2 sequences. Bithynia siamensis siamensis was found in almost all sampling localities, with different quantities and detected frequencies. From a total of 7473 B. s. siamensis specimens, O. viverrini s.l. infections were detected in the Northern Bangkok, Muang Nakhon Pathom, Krathum Baen, and Lam Luk Ka areas with an overall prevalence of 0.05% (4/7473) and prevalence of 0.22% (1/455), 0.21% (1/469), 0.40% (1/253), and 0.16% (1/614) in individual localities with positive snails, respectively. This study is the first investigation of digenean infection in the canal network system-type habitat in Thailand and revealed extremely low O. viverrini s.l. prevalence.