Collection of sponges (Porifera) originates from Hungarian Royal Biological Station, which was operative in Rijeka from 1905 till 1918. Part of the material had been collected during fieldwork with the vessel “Bios”. Since 1987., materials have been collected in the process of autonomous diving along transects. Biological material in collections is stored in the form of wet and dry preparations Computer database of the collection has been kept since 1997. Collection of sponges has been added to the Registry of Cultural Property of Republic of Croatia under number 4438.

Collection of cnidarians (Cnidaria) originates from Hungarian Royal Biological Station, which was operative in Rijeka from 1905 till 1918. Part of the material had been collected during fieldwork with the vessel “Bios”. Since 1987., materials have been collected in the process of autonomous diving along transects. Biological material in collections is stored in the form of wet and dry preparations Computer database of the collection has been kept since 1997. Collection of cnidarians has been added to the Registry of Cultural Property of Republic of Croatia under number 4438.

Collection of annelids (Annelioda) originates from Hungarian Royal Biological Station, which was operative in Rijeka from 1905 till 1918. Part of the material had been collected during fieldwork with the vessel “Bios”. Since 1987., materials have been collected in the process of autonomous diving along transects. Biological material in collections is stored in the form of wet preparations Computer database of the collection has been kept since 1997. Collection of annelids has been added to the Registry of Cultural Property of Republic of Croatia under number 4438.

The Malacological collection holds 10000 specimens of gastropods, bivalvia and cephalopods. The bivalvia collection is, according to experts, a collection of B category, since out of 224 known Adriatic species, after the invertebrate list published in 1997, it contains 135 species from the northern Adriatic, some of them identified in the aquatorium for the first time. In the period 1987 - 1999 the bivalves for the malacological collection were collected during autonomous diving within the scope of Biocenological research of the western coast of the island of Krk, of the Vinodol channel, Rijeka bay, and islands of Goli, Prviæ and Grgur. Since 1997, when Mirjana Legac retired, the curator Milvana Arko-Pijevac, B.Sc. manages the malacological collection. Since 1997 the collection has been entered in computer database. The Malacological collection has been added to the Registry of Cultural Property of Republic of Croatia under number 4438.

The Crustacea Collection originated in the specimens from the Hungarian Royal Biological Station as well (200 inventory numbers). In 1997 a curator carcinologist took care over it. Biological material collected along the diving transects of the Primorsko-goranska County and entire Adriatic is constantly added to the collection. A significant part of the collection today is represented by the material collected during the biological fishing expedition Hvar in 1948-1949 (Decapods). The collection is entered in the computer database; 1534 inventory numbers of the groups Cirripedia, Stomatopoda, Decapoda, Isopoda and Amphipoda have been entered so far. The two decapod species from the collection ( Brachycarpus biungiuculatus and Hippolyte prideauxiana) were identified as a new species for the Adriatic in 2003. and 2005.

Collection of Bryozoa (Bryozoa) originates from Hungarian Royal Biological Station, which was operative in Rijeka from 1905 till 1918. Part of the material had been collected during fieldwork with the vessel “Bios”. Since 1987., materials have been collected in the process of autonomous diving along transects. Biological material in collections is stored in the form of wet and dry preparations (animal skeletons).Computer database of the collection has been kept since 1997. Collection of tunicates has been added to the Registry of Cultural Property of Republic of Croatia under number 4438.

Collection of Echinoderms (Echinodermata) originates from Hungarian Royal Biological Station, which was operative in Rijeka from 1905 till 1918. Part of the material had been collected during fieldwork with the vessel “Bios”. Since 1987., materials have been collected in the process of autonomous diving along transects. Biological material in collections is stored in the form of wet and dry preparations. In 1995. the collection was revised by specialist Dr. Dušan Zavodnik.Computer database of the collection has been kept since 1997. Collection of Echinoderms has been added to the Registry of Cultural Property of Republic of Croatia under number 4438.

Collection of Tunicates (Tunicata)) originates from Hungarian Royal Biological Station, which was operative in Rijeka from 1905 till 1918. Part of the material had been collected during fieldwork with the vessel “Bios”. Since 1987., materials have been collected in the process of autonomous diving along transects. Biological material in collections is stored in the form of wet and dry preparations Computer database of the collection has been kept since 1997. Collection of Bryozoans has been added to the Registry of Cultural Property of Republic of Croatia under number 4438.

Collection of other marine invertebrates originates from Hungarian Royal Biological Station, which was operative in Rijeka from 1905 till 1918. Part of the material had been collected during fieldwork with the vessel “Bios”. Since 1987., materials have been collected in the process of autonomous diving along transects. Biological material in collections is stored in the form of wet and dry preparations Computer database of the collection has been kept since 1997. By the principle of separation of collections based on the systematic groups of organisms, small groups with few species are added to a collection of other marine invertebrates. Over time, with the increase in the number of types and instances of the aforementioned groups, there is a possibility of establishment of new collections.

Ichthyological collection was, as well as other collections the Museum currently houses, established in 1945 by collecting the specimens of the dissolved Hungarian Royal Biological Station, City Museum (Museo Civico), and various schools in Rijeka. Also, new specimens were added to the collection. In 1992 a curator ichtiologist took over the collection and the number of newly acquired specimens increased rapidly. There are wet and dermoplastic preparations, skeletons or their parts and jaws in the collection. The collections holds about 3500 specimens for 350 species. Especially valuable specimens of the collection are species of goby fish that can only be found in few museums in the world. Among them types of the Gobius kolombatovici Kovačić and Miller species should be singled out. The fish is 10 - 12 cm long, and belongs to the goby family (Gobiidae). It is of characteristic color, and has longitudinally arranged orange spots, with a black spot on the first dorsal fin. In 1998 it was discovered in four localities along the east coast of the island of Krk. It lives at the depth of 15 - 38 meters, on the sea floor composed of detritic sand, fine gravel and stones, most often along steep underwater rocks. Not much is known about the species, as is the case with most of the Mediterranean goby fish, many of which were described already in the 19th century.

Collection of amphibians and reptiles of the Natural History Museum Rijeka was, just like other collections of the Museum, established in 1945 by the collection of materials of the former Hungarian Royal Biological Station, as well as the materials from the former City Museum (Museo Civico) and from various schools in Rijeka. Later on, the Collection has been updated with newly gathered specimens. In the Collection, there are wet preparations, dermoplastic preparations and skeletons. The collection holds 227 specimens and 61 species. Part of the Collection is displayed in the permanent display of the Museum. The most recent revision was made by Mrs. Irena Grbac in 1999. Computer database of the Collection has been kept since 1999.

Ornithological Collection of the Natural History Museum Rijeka was, just like other collections of the Museum, established in 1945 by the collection of materials of the former Hungarian Royal Biological Station, as well as the materials from the former City Museum (Museo Civico) and from various schools in Rijeka. Later on, the Collection has been updated with newly gathered specimens. In the Collection, there are wet preparations, dermoplastic preparations and skeletons. Part of the collection is displayed in the permanent display of the Museum. The collection holds 261 specimens and 157 species. The most recent revision was made by Mrs. Jelena Kralj, Ph.D. and Mr. Dragan Radović. in 1998. Computer database of the Collection has been kept since 1998.

Collection of mammals of the Natural History Museum Rijeka was, just like other collections of the Museum, established in 1945 by the collection of materials of the former Hungarian Royal Biological Station, as well as the materials from the former City Museum (Museo Civico) and from various schools in Rijeka. Later on, the Collection has been updated with newly gathered specimens. In the Collection, there are wet preparations, dermoplastic preparations, skeletons and skeleton fragments. The collection holds 117 specimens and 60 species. Part of the Collection is displayed in the permanent display of the Museum. The most recent revision was made by Mrs. Marijana Vuković and Mrs. Maja Baltić in 1999. Computer database of the Collection has been kept since 1999.

Collection of algae consists out of 255 samples: 205 herbarium and 50 wet preparations. One hundred samples of algae were gathered from 1881. – 1882. in the Rijeka Bay area (Lovran, Ika, Opatija, Rijeka, Bakar, Kraljevica). Other samples were gathered periodically from 1963. – 1966., 1981. – 1982. and in 1992. Since 1995, algae have been stored as wet preparations.

Herbarium Collection has been founded in 2003, since when plant material is being collected mostly through field work and collecting excursions, and, in minor extent, by donations and exchanging material with other herbarium collections. Museum items in this collections mostly originate from Croatia, Slovenia, Italy, Bosnia and Herzegovina, Montenegro, Romania, Serbia, Albania, FYR Macedonia, Turkey, Greece, Austria, Switzerland etc. Specimens are collected in a way to allow further scientific research through both classical and modern, molecular and genetic methods. The collection holds a holotype of a newly described species Edraianthus pulevicii Surina & D. Lakušić and many topotypes, as well as some of the world's most comprehensive collections of spcimens of genera Edraianthus (Campanulaceae), Wulfenia (Plantagininaceae), Athamanta (Apiaceae) and Drypis (Caryophyllaceae). The significance of the collection has been affirmed also through it being registered in the world register of herbari Index herbariorum under the acronym NHMR.

Collection of wet botanical preparationsis the most recent collection of the Museum – dating to 2008. Since that time, botanic curator has been taking care of the Collection that consists out of approximately 10 museum items. Plant specimens from a wider Rijeka region are being collected and stored in the form of wet preparations (alcohol, formaldehyde). Documentation of the Collection is being kept in computer database.

The Collection of Minerals holds various minerals from typical localities in the world, systematically arragned based on their chemical structure. Systematic classification gives an insight into a variety of shapes and sizes of one and the same kind of mineral from different paragenetic localities. Valuable are specimens of different crystals of quartz, specimens of crystals of ore minerals and gemstone jewellery.

The Collection of Rocks holds various litospheric rocks systematically arranged into groups of magmatic, sedimentary and metamorphic rocks. All kinds of both, building and decorative stones of the Rijeka region are presented (Jurassic, Cretaceous, Paleogene limestones and breccias; Triassic andesite). The collection holds the oldest object in the Natural History Museum in Rijeka - a specimen of silicic sedimentary rock composed of flint found in 1872 on Iceland. There is also a specimen of travertine, found in 1892 at the Plitivice Lakes, Croatia.

The Evolution of Man Collection consists of moldings (copies) of the bones of the representatives of the hominid's evolutionary stages (Australopithecus, Homo habilis, Homo erectus, Homo sapiens neanderthalensis), moldings of their artefacts, of the fossil fauna of the period, and original skull bones of modern man (Homo sapiens sapiens).

The Geological Stratigraphic Collection of the Rijeka Region holds various rocks and fossils which reveal the litologic structure and biostratigraphy of the deposits of the Rijeka region from the oldest rocks dating back to Carbon to the youngest that sedimented during Paleogene. Important are specimens of ore resources of the Rijeka region.

The Collection of Quarternary Fossil Fauna from the Caves of the Rijeka Region holds numerous fossil bones and teeth discovered in 25 caves, thus supporting the diversity of the Peistocene animals. The Collection also holdsawell preserved cave bear skull (Ursus spelaeus ROENMULLER & HEINROTH) found in Sparožna cave in the Kastav area, a skeleton of a fossil brown bear (Ursus arctos LINNE) found in the Banić cave on the island of Cres, and artefacts of Peleolithic and Mesolithic cultures.