The forest at Ba Be can be classified into two main types: limestone forest and lowland evergreen forest. The limestone forest is distributed on steep limestone slopes with shallow soil, and covers a large proportion of the national park. This forest type is dominated by Burretiodendron hsienmu and Streblus tonkinensis. Lowland evergreen forest is distributed on shallow slopes with deeper soils. This forest type has a higher tree species diversity than limestone forest and has a richer ground flora.
With regard to mammals, the site is of particular interest for the presence of the globally vulnerable Owston's Civet Hemigalus owstoni and Francois's Leaf Monkey Trachypithecus francoisi, although it appears that only one group of 7 to 13 Francois's Leaf Monkeys remains.
It is highly unlikely, however, that the globally critically endangered Tonkin Snub-nosed Monkey Rhinopithecus avunculus continues to occur within the core zone of Ba Be National Park. Information from Ba Be National Park staff suggests that the species may have occurred in the north-west of the national park as recently as 1997.
However, surveys by BirdLife International and Fauna & Flora International on behalf of the Creating Protected Areas for Resource Conservation Using Landscape Ecology (PARC) Project, in 2002 and 2003, provided no evidence in support of the supposition that the species remains at Ba Be.
Ba Be is unique amongst Vietnamese protected areas for the diversity of freshwater habitats. This is reflected to some extent in the diversity of fish species found at the site. Although recent surveys by the PARC Project have documented the existence of several endemic fish species, more work needs to be conducted in this area.
Ba Be also supports a high butterfly species richness. During surveys in 1997 and 1998, a total of 332 species were recorded at the national park, of which 22 were new records for Vietnam.