Bönigen lies in the Bernese Oberland on the south-west side of Lake Brienz, near to the point where the Lütschine flows into the lake. The village centre lies in the northwest part of the municipality along the Lütschine and up to the lake. The village has grown towards the nearby resort town of Interlaken, and the built-up areas are nearly contiguous. The majority of the municipal area is located on the steep mountainsides, where such peaks as the Loucherhorn (), the Roteflue () and the Schynige Platte are found.