This paper analyzes flood impact on the historical objects and cultural heritage in Southern and Eastern Serbia. The basic research problem is the lack of systematized databases regarding the flood impact on the cultural heritage, in addition to the lack of official manuals or other types of educational material dealing with the management of the assets with monumental properties in flood situations. The goal of the paper is to indicate this problem to the professional and wider public through systematization and classification of the observed damages on the buildings. The paper first provides a brief overview of the development of flood protection throughout history with particular reference to the research area. In addition, the history of floods in Serbia is also analyzed in order to point to the frequency and scale of this problem in the researched area. Through the research of archival materials in the appropriate institutions as well as direct recording of assets in the field, the degree of flood impact on historical objects in the territories of Southern and Eastern Serbia is determined. It refers to both declared cultural monuments and those that are still undeclared but possess certain monumental properties. Only the material damages on the immovable cultural assets have been analyzed. The protection of the movable cultural assets has not been taken into consideration, although it represents a very important aspect of every flood damage. A classification of the damages observed on these types of buildings, which occur as a direct or indirect consequence of floods, has been carried out. Examples of structural damage are presented in the paper (such as fissures, cracks, bucklings and collapse of parts or overall objects). Examples of the damages that do not threaten the stability of buildings are also presented. Here, they are divided into two groups—moisture-induced damages and biodegradation. The paper also gives examples of the damages induced by direct or indirect impacts of floods. It is from these examples that general lessons can be drawn, namely those that would be applicable to the endangered categories of cultural heritage. The classification is conducted for the purpose of better planning of preventive or rehabilitation strategies and measures for the preservation of architectural cultural heritage. Recommendations for dealing with heritage assets in the case of floods are also given.