Japan possesses a large number of natural wetlands, although most have been adversely affected by development in recent decades. Most of its lakes are very small, Lake Biwa in central Honshu being a notable exception, it is one of the few lakes in Japan of pre-glacial origin. There are several other large lakes, mostly of volcanic origin, in Hokkaido.

Extensive freshwater marshes still persist in some of the most remote areas, particularly in eastern Hokkaido and contain the majority of the country's coastal lagoon and salt marsh systems of which Lake Furen is the largest. Elsewhere, most of the lowland, marshy habitats and coastal lagoons have been drained for agricultural land.

Japan's largest areas of intertidal mudflats are in estuaries and bays along the Pacific coast, such as the Bay of Tokyo and Inner Iisa Bay, where there are particularly large tidal ranges, but much of this habitat has been lost to development. Mangrove swamps are confined to the Amami Island and Ryukyu Island in the south.

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