Bottmingen has an area, as of 2009, of 2.99 square kilometers (1.15 sq mi). Of this area, 0.77 km2 (0.30 sq mi) or 25.8% is used for agricultural purposes, while 0.55 km2 (0.21 sq mi) or 18.4% is forested. Of the rest of the land, 1.61 km2 (0.62 sq mi) or 53.8% is settled (buildings or roads), 0.02 km2 (4.9 acres) or 0.7% is either rivers or lakes and 0.01 km2 (2.5 acres) or 0.3% is unproductive land.
Of the built up area, industrial buildings made up 1.3% of the total area while housing and buildings made up 34.8% and transportation infrastructure made up 12.0%. Power and water infrastructure as well as other special developed areas made up 1.7% of the area while parks, green belts and sports fields made up 4.0%. Out of the forested land, all of the forested land area is covered with heavy forests. Of the agricultural land, 14.0% is used for growing crops and 5.0% is pastures, while 6.7% is used for orchards or vine crops. All the water in the municipality is in lakes.
The blazon of the municipal coat of arms is described as "Two crossed figures on a red background whose meaning cannot be determined with certainty. It is the seal of the Basel aristocrat Schilling, the second owner of the Bottmingen castle."