Extensive forests throughout Alam-Pedja Nature Reserve include swamp forests, carrs, floodplain and wooded meadows (with oak) and alluvial broad-leaved forests that are of particular botanical value. The species diversity in these alluvial Alnus glutinosa - Ulmus laevis –U. glabra forests is high; these forests - as relicts - have persisted in only two other places in Estonia.
Integral complexes of five mires are separated by unregulated rivers with floodplain meadows. The mires are represented by bogs (Põltsamaa, Umbusi), fens (Karisto, Ulila), transition bogs, and their complexes (Laeva). These bogs are of a continental type, with abundant bog-pools. Large areas are covered by permanently wet, birch-dominated swamp forest without any drainage.
The Alam-Pedja Nature Reserve is rich in different landscape types, including different wetland ecosystems: large and small rivers, oxbow meanders and mires with their typical water regime. Large tributaries of the Emajõgi River (Pedja, and Põltsamaa Rivers) and smaller tributaries form an integral hydrological system. These systems form many transition zones (ecotones) between different habitats and are usually the most species rich areas. Thus, the biodiversity of the area is closely connected with the diversity of soils, landscapes and hydrological regime.
The climate of the area is in a zone of transition from a maritime to continental climate, and is influenced heavily by nearby Võrtsjärv Lake in the south and the Sakala uplands to the north. Mean annual temperature is 4.5°C, precipitation averages about 560 mm per year, and snow cover lasts approximately 110 days, with rivers and lakes covered with ice from December until April. Regular and predictable floods cover large areas and last for relatively long periods of time. Flooding typically occurs during spring, and during autumns with high precipitation. Such flooding does do not occur elsewhere in Estonia or in the other Baltic States. These floods have formed the natural alluvial sediments and relief forms present in the Alam-Pedja Nature Reserve today. The hydrological cycle is important for the recharge and discharge of groundwater, and for the maintenance of water quality. Further, there are very few similar regions where the natural hydrological system has been as well preserved within Europe. Thus, Alam-Pedja, due to its large territory and natural hydrological regime, is of national and international importance.
640 species of fungi have been recorded within the reserve which includes 135 species found primarily in Estonia, and includes one recent new discovery (Tremella estonica), and 9 species listed in the Red Data Book of Estonia. 158 species of lichens (Lichenes; 2 species in the Red Data Book of Estonia), and 184 species of bryophytes (Bryota) have been recorded within the reserve (7 species listed in the Red Data Book of Estonia), although most of the bryophytes have not yet been completely inventoried. 485 species of vascular plants have been recorded, including 433 species of herbs and 52 species of trees and shrubs. 15 vascular plant species are listed in the Red Data Book of Estonia.
22 species of mollusks (Mollusca) have been recorded in the meanders, ditches and rivers of the Reserve. 32 species (54 in Estonia) of dragonflies (Odonata) are found in the reserve and potential suitable habitat could mean that 40 dragonfly species live in the reserve of which 2 species are listed in the Red Data Book of Estonia. 410 species of butterflies and moths (Lepidoptera) have been recorded (about 900 in Estonia), and more than 100 species of beetles (Coleoptera) have been found, mainly long riverside areas and river floodplains. Blethisa multipunctata and Pterostichus anthracinus are abundant beetles in the reserve, yet rare within the rest of Estonia, and 2 species (Leptura nigripes and Agrilus mendax) are listed in the Red Data Book of Estonia. 25 species of fish (Ichyhyes) have been caught (number of fish species may even reach 30). The floodplains and old river beds are important spawning sites for various fish species such as Aspius aspius, Siluris glanis, Abramis brama and Esox lucius. The reserve is home to 6 species of amphibians (Amphibia) and 3 species of reptiles (Reptilia).
Alam-Pedja Nature Reserve is the most important breeding area for Great Snipe (Gallinago media) in Estonia, which also supports a rich assemblage of breeding species of mire, forest and wetland, notably the globally threatened Greater Spotted Eagle (Aquila clanga). Breeding species of global conservation concern that do not meet IBA criteria include White-tailed Eagle (Haliaeetus albicilla; 2 pairs). Significant proportion (about 1%) of national population breeding at Alam-Pedja include European Honey-buzzard (Pernis apivorus; 5-7 pairs), Black Tern (Chlidonias niger; 150-200 pairs), Eurasian Nightjar (Caprimulgus europaeus; min. 20 pairs), Gray-faced Woodpecker (Picus canus; min. 15 pairs). Numbers of breeding Black Grouse (Tetrao tetrix; min. 75 pairs) are also notable. A total of 193 bird species have been observed in the reserve (153 breeding, 24 transit migrants, and 14 vagrants or others). Of these, 35 species are listed in the Red Data Book of Estonia and 40 species are listed in Annex I of the Bird Directives.
43 species of mammals have been recorded in the reserve. Many small mammals can be found within the reserve including the East European Hedgehog (Erinaceus concolor), 4 species of shrews including the rare Musked Shrew (Sorex caecutiens), and the Lesser Weasel (Mustela nivalis). 8 of the 11 bat (Vespertilionidae) species found in Estonia are present in Alam-Pedja Nature Reserve, and most notably healthy populations of the Pond Bat (Myotis dasycneme). Large mammals breeding in the reserve or rare or protected in other parts of Europe include the otter (Lutra lutra), Stoat (Mustela erminea), wolf (Canis lupis), bear (Ursus arctos), and lynx (Felis lynx). Elk (Alces alces), roe deer (Capreolus capreolus), and wild boar (Sus scrofa) are common as well as non-native raccoon dog (Nyctereutes procyonoides) and American mink (Mustela vision) species. 5 mammal species present in the reserve are listed in the Red Data Book of Estonia.