The shape of Los Baños resembles the back of a fist. Its habitable area rests on the narrow southern shoreline of Laguna Lake and northern foothills of Mt. Makiling. Mount Makiling, with an elevation of 1,090 meters (3,633 ft.) above sea level, dominates the whole town and is traversed by five rivers, namely: Dampalit, Saran, Pili, Mulawin and Maitim, which all drain to Laguna Lake.
Another prominent feature at the northwest tip of the town is the Alligator Lake in Brgy. Tadlac. The lake, contained in a raised circular shape with a diameter of about 330 meters (1,100 ft.), is believed to be the mouth of an extinct volcano that juts out of Laguna Lake. The lake’s water level is higher than that of Laguna Lake.