Areas subject to little anthropogenic impact and with preserved river dynamics are very rare in the floodplains of large European rivers [7-9]. These environmentally valuable territories are usually categorized as different forms of protected areas. Particularly due to the establishment of the Natura 2000 network of nature protection areas, the number of floodplain forests thus protected in Europe has been gradually increasing. In the context of environmental assessment of Natura 2000 sites, environmental assessment of the level of natural habitat conservation appears to be a potential decision support tool. This paper assesses the efficiency of the Natura 2000 European Network in the biodiversity conservation of Central European floodplain forest habitats on the ecosystem level of an entire river basin (Morava River basin, Czech Republic). In order to express the efficiency of natural habitat conservation, our paper uses the nature conservation efficiency index, which is calculated in the GIS environment based on an environmental analysis of data obtained through natural habitat mapping in the Czech Republic, conducted in 2001–2004 as part of the conservation objectives of Natura 2000. Environmental analysis results show that the conservation efficiency of the Natura 2000 network in territorial conservation of floodplain forests in the study area of the Morava River floodplain is approximately six times as high (NCEIEU = 0.067) as the efficiency of the Czech national network of protected areas (NCEICZ = 0.017). The paper also highlights the importance of detailed habitat mapping for environmental landscape studies.