It is situated on the borderline between two geographical regions: the Sandomierz Basin (Kotlina Sandomierska) in the northern part of the commune's territory, and the Wieliczka Piedmont (Pogórze Wielickie) in the southern part.

Its territory extends over about 50 km along the Raba and Stradomka rivers and their tributaries.

The commune is cut almost in half by the E40 Dresden-Kraków-Lvov International Road, a railway line.

The area contains flat fields and meadows of the Raba river valley in the north, including the Niepołomice Forest (Puszcza Niepołomicka); and a mountainous area in the south, within sight of the Beskid Wyspowy mountain range.

Gmina Bochnia contains the villages and settlements of Baczków, Bessów, Bogucice, Brzeźnica, Buczyna, Cerekiew, Chełm, Cikowice, Dąbrowica, Damienice, Gawłów, Gierczyce, Gorzków, Grabina, Krzyżanowice, Łapczyca, Majkowice, Moszczenica, Nieprześnia, Nieszkowice Małe, Nieszkowice Wielkie, Ostrów Szlachecki, Pogwizdów, Proszówki, Siedlec, Słomka, Stanisławice, Stradomka, Wola Nieszkowska, Zatoka and Zawada.