The city is in the northeast region of Shiga Prefecture. Its area occupies 5.1% of Shiga's total land area. The west end of the city fronts Lake Biwa, while the mountainous east side borders on Sekigahara, Gifu Prefecture.
Mt. Ibuki is in the northeastern part of the prefecture. It is Maibara's most prominent landmark and designated as one of Japan's 100 most famous peaks. The Anegawa River and Amanogawa River empty into Lake Biwa and about 70 percent of the city comprises forest land. The city thus boasts an abundance of water and greenery.