The cornerstone of the botany and mycology collections featured in the museum is the herbarium (comprised of over 150 thousand units) and the finds of prominent botanists such as Karl Reinhold Kupffer, Ferdinand Erdmann Stoll, Nikolai Malta and others.

Major minerals found in Latvia, such as gypsum, dolomite, limestone, tufa, clay, sand and gravel, are widely represented in the geology collections. Pride of place in the palaeontology display is given to unique finds of armoured fish from the Devonian period.

Various animal groups are covered in the display of the zoological collection, including sponges, corals, molluscs, echinoderms, insects, spiders, crustaceans, fish, amphibians, reptiles, birds and mammals.