Lake Tonle Sap, the largest lake in Southeast Asia, has been closely associated with the lives and culture of Cambodian people and society. A great amount of aquatic resources arising from its high biodiversity has supported them since the Khmer Dynastic Time to the present. However, because problems of environmental pollution, and atmospheric pollution in particular, have become worse within a short space of time in Cambodia due to rapid development of tourism of the Angkor Monument Complex for instance, its harmful effect to the natural environment has been of recent concern. Rapid deterioration of the natural environment will probably trigger a certain change of the lake ecosystem, and the change might lead to a fatal damage to the plentiful aquatic resources. The present article describes the preliminary results of the research missions “Evaluation of Mechanisms Sustaining the Biodiversity in Lake Tonle Sap” from 2003 to 2005. On the basis of these results loss and damage of the natural environment and biodiversity of the lake are estimated, along with the progress of atmospheric pollution.