Neighboring districts are (from the north clockwise) Tha Muang and Tha Maka of Kanchanaburi Province, Kamphaeng Saen and Mueang Nakhon Pathom of Nakhon Pathom Province, and Photharam of Ratchaburi Province.
Ban Pong District is hilly in the very western part of the district, while the eastern part is flooded plain with the Mae Klong River running through the city centre, connecting the city to the Gulf of Thailand.