Lake Biwa, the largest lake of Japan, is located in central Honshu and fills the bottom of an oblong tectonic basin. The lake was formed some five million years ago and is therefore one of the oldest lakes in the world geologically, though it was originally located some distance south and moved gradually to its present site about 700,000 years ago. The long history of isolation from other water bodies is suggested by the lake's biota, which is fairly rich for an island lake, containing about 50 species of fish, 40 species of mollusca and a number of indigenous species.

Lake Biwa measures 63.5 km from north to south and is strongly constricted at about 16 km from its southern end reaching a minimum width of only 1.35 km. The deep main basin (average depth 44 m) north of the constriction is called the Northern Lake, while the shallow sub-basin (average depth 3.5 m) to the south is called the Southern Lake. The two basins differ considerably in water quality, physical conditions, flora and fauna.

The lake's catchment area is 4.7 times as wide as the lake itself, and corresponds closely to the administrative limits of Shiga Prefecture. Forest-covered hills and mountains accounts for nearly 60% of the land area of the Prefecture, and farmlands (mostly wet paddy fields) makes up additional 25%. The forest vegetation consists mostly of secondary forests of pine on low hills and of mixed deciduous hardwoods on marginal mountains, and plantations of conifers. There are several cities of moderate size, the largest being Otsu with a population of 240,000.

Lake Biwa is also the biggest water resource in Japan that supplies city and industrial water for some 13 million residents in Osaka/Kyoto/Kobe megalopolis. The quality of lake water was profoundly influenced by economic development since the 1960's through rapid eutrophication. The legal control of waste water discharge from industries implemented by the National Government in 1970 slowed down the rate of eutrophication to a certain extent, but the steady increase of population, ever-rising standard of living, increased fertilizer application, etc. in the catchment area combined to result in a slow but steady march of lake water quality degradation.

The Shiga Prefectural Government enacted in 1980 the Ordinance for the Prevention of Eutrophication of Lake Biwa, which, for the first time in this country, prohibited the use of phosphate-containing synthetic detergents. The phosphorus content of lake water was thereby reduced considerably, but the effect of reduced phosphorus loading on biological processes in the lake is not yet apparent. In December 1985 Lake Biwa was appointed as one of the first five designated lake based on the Law Concerning Special Measures for Preserving Lake Water Quality, along with Kasumigaura, Inba-numa, Tega-numa, and Kojimako. (1987, revised in 2018)

Serious issues regarding the natural ecosystem is that the intrinsic ecosystem of the Lake Biwa is being reduced such as reducing number of native fishes, increasing number of invasive nonnative fishes and thick growth of waterweed.

The Shiga Prefectural Government executed the Comprehensive Conservation and Development Plan of the Lake Biwa (Mother Lake 21 Plan) in 2000, taking the ideal state of the Lake around the year 2050 into consideration. Various efforts since then include the water quality improvement, the development of water source, and conservation of natural environment and the scenery of the landscape.

In 2011 the Plan went through a complete revision and under the keyword of "consideration to the relationship" more comprehensive measures have been taken with a view of the whole basin as one system. And the community named "Mother Lake Forum" is created and various entities including local governments, residents, NPO, researchers and corporation are managing the progress of the plan together.

The Law Concerning the Conservation and Rehabilitation of Lake Biwa was promulgated and enforced on September 28, 2015. The purpose of the law is to contribute to the conservation and rehabilitation of Lake Biwa, a national asset as a sound and abundant lake, thereby future generation can enjoy the benefits the lake provides with.

According the the law, the Shiga Prefectural Government executed the Lake Biwa Conservation and Rehabilitation Plan. And the various efforts are going on based on the plan, including water quality improvement activities and promotion of environmental education. (March 2018)