The Lake Biwa Museum has a large research section, employing researchers covering many aspects of the cultural, faunal and floral aspects of lakes and their watersheds.

Director General
Toru Shinohara Folkloristics - Folklore related to the relationships between people and nature.

Vice Director
Keiichi Takahashi Vertebrate palaeontology - The transformation of ancient vertebrates in East Asia as viewed in elephant fossils.

Cultural History and Geoscience Research Group
Chiyomi Yamakawa Palaeobotany - Fossil flora of the Cenozoic.
Yasufumi Satoguchi Geology - Volcanic ash layers in the Kobiwako Group, and the correlation with volcanic ash layers in other areas.
Michinori Hashimoto History - Social changes in the 13th century of Japan.
Ping Yang Environmental sociology - Relationships between nature and humans.
Ryoma Hayashi Paleo-microbiology - Quaternary vegetation changes based on pollen analyses.
Mika Okubo Regional environmental sociology - Transformation of lifestyles in rural communities.
Takeshi Kitai Potamology - Sediment transport of the Echigawa River.
Keiichi Watanabe Folkloristics - Village and 'miyaza' folkloristics.
Yusuke Senoo Archaeology - Archaeological research on the beginnings of rice cultivation and farming culture in the Japanese archipelago.
Ryoichi Tabata Ichthyology

Biotic and Human Interaction Research Group
Kayoko Kameda Animal ecology - The role of birds in the ecosystem.
Hiroki Haga Limnology - Lake ecosystems and the interaction of the environment.
Katsuro Yahiro Systematics of terrestrial insects - Taxonomy and ecology of Caraboidea beetles.
Masanari Matsuda Benthonic zoology - Investigation of bivalve distribution in Shiga Prefecture.
Masayuki Kuwahara Fish ecology - Relationship between Biwa trout, a subspecies indigenous to Lake Biwa, and 'amego' or red-spotted masu salmon inhabiting Lake Biwa's tributaries.
Katsuki Nakai Environmental conservation and restoration - Ecosystem of the littoral zones of lakes, ecology of introduced aquatic organisms; geographical variation of land snails.
Kazuhiro Masunaga Aquatic insects - Classification and systematic evolution of aquatic insects, biogeography.
Robin James Smith Aquatic microfauna - Taxonomy and ecology of freshwater ostracods. Ontogeny and evolution of ostracods.
Takahide Kudamatsu Agriculture - Argricultural engineering and administration.
Minako Ashiya Aquatic botany - Breeding and growth of aquatic plants.
Yoshitaka Kataoka Fisheries science
Ayami Yamamoto Forestry
Takahito Suzuki Microbiology - Planktonic and benthic microorganisms of the Lake Biwa watershed.

Museum Studies Research Group
Takashi Toda Museum information and computer science - Investigating the water flows of Lake Biwa through satellite and aircraft observations.
Taisuke Ohtsuka Microbiology - Distribution of adhesion diatoms.
Shigefumi Kanao Aquatic propagation - Ecology and conservation of fish that use rice fields.
Kumiko Sawabe Museology - Regional cooperation of museums.
Yuko Matsuoka Aquatic fauna - Physiology and ecology of Baikal seals.
Tomoyuki Okuno School cooperation
Hidemasa Kobayshi School cooperation - Improving school cooperation

Honorary Researchers
Hiroya Kawanabe Ecology - Relationship among ecological complexity and biological and cultural diversities.
Tomoo Nunotani Museology - Past-environment reconstruction utilizing wooden relics. Management of the museum from the users' point of view.
Tsuneo Nakajima Morphology of fossil fish - Pharyngeal teeth of fishes of the carp family.
Masayoshi Maehata Aquatic propagation study - Breeding and ecology of catfish.
Masaharu Yoda Archaeology - Process of state formation.
Mark Grygier International limnology - Crustacean systematics and marine parasites.