Spring water from the bottom of Lake Biwa is thought to affect the lake’s environment, but the actual state of deep lake bottom spring water has not been clear. In 2009, the deep lake bottom spring water containing over 99% methane gas was discovered near the deepest part of the northwestern region of Lake Biwa, raising concerns about its effect on the lake bottom environment. However, since 2013, investigations of the spring water have not sufficiently been conducted. We have been conducting underwater acoustic surveys, water quality and temperature surveys, temperature surveys of lake bottom sediments, and gas analysis since 2020 with the aim of clarifying the actual conditions of the deep lake bottom spring water and its effect on the lake bottom environment. As a result, Acoustic anomalies （gas acoustic anomalies） attributed to gas emissions from the lake bottom were found to be widely distributed in the lake bottom at depths of 60 meters or more in the northwestern part of Lake Biwa. Water quality and temperature surveys indicated that the effect of the deep lake bottom spring water on the lake bottom environment is likely insignificant, and it was determined that the primary component of the gas, methane, originates from organic sources in the lake bottom sediments. In the place where the gas acoustic anomalies continue to be observed, the temperature gradient in the lake bottom sediments is large. It is plausible that groundwater, which finally emerges from the lake bottom as the spring water, is supplying heat to the lake bottom sediments. Based on the above, we have considered the generation mechanism of the spring water and gas from the deep lake bottom of Lake Biwa.