Within implementation of Directive of the European Parliament and of the Council 2007/06/ES of 23 October 2007 on the assessment and management of flood risks the classification was recommended to Czech Republic which sorties the areas affected by floods according to the degree of threat and economic potential of these areas. For this purpose was developed the model of territory unit evaluation. This model is formulated as a combination of two models including model of risk matrix and model of the area value expressed by available statistical data. These data reflect the different levels of areas development and their possible future development through weighted multi-criteria decision making. The aim of our paper is to present the model and its use in terms of increasing the efficiency of spending resources in area in relation to flood protection. The model may serve as an inspiration in terms of use for such a large territorial units in European countries applying the Directive.