On 17 January 2017, the Lake Biwa Museum signed a Memorandum of Understanding with the Hydrobiological Institute, Ohrid, Macedonia, to cooperate in the research of ancient lake systems.
Similar to Lake Biwa, Lake Ohrid, in Macedonia and Albania, is an ancient lake, with a history stretching back five million years.
Since 2016, the Lake Biwa Museum has been cooperating with the Nakdonggang National Institute of Biological Resources, Korea, on freshwater biodiversity research.
This has involved joint fieldwork to collect shrimps in Lake Biwa, the Pacific coast of Japan and the Sea of Japan, joint research on the phylogeography of freshwater fish in Korea and Japan, and joint research seminars. The latest seminar, Freshwater Biodiversity and the Changes in Korea and Japan, took place on 4-7 December 2018 at the Lake Biwa Museum, and was supported by JSPS and NRF under the Japan - Korea Basic Scientific Cooperation Program.
The Lake Biwa Museum and the Baikal Limnological Museum signed a cooperation agreement in 2014. Since the summer of 2016, the museum has been exhibiting fish, amphipods and seals from Lake Baikal.
As a result of collaborative efforts, a special exhibition "The Hometown with Abundant Fisheries, Agriculture + Silk" was held in the Lake Biwa Museum between 19 July and 24 November, 2014.
In 2002 the Museum agreed to cooperate with the Institute of Hydrobiology, Chinese Academy of Sciences, in particular on research of carps in East Asia.
From the 14 July to 25 November 2007, the museum held a special exhibition "The Story of Carps in the Lake Biwa Region - Illustrating People's Ties to Lakes in East Asia" based on this research.
The Lake Biwa Museum has cooperated with the National Museum of Natural History in Paris since 1998.
With the cooperation of the National Museum of Natural History, the Museum held a special exhibition "Learning with Fabre. A Century after Fabre's "Souvenirs Entomologiques"" from 29 April to 31 August 2008.