The paper presents a case study comparing values of two internationally significant wetland areas: Obedska Bara in Serbia and Lonjsko Polje in Croatia, using the Wetland Assessment Model (WAM). The model is used to highlight differences and similarities between biological, ecological, educational, public awareness and aesthetic values of the two selected study areas. The model requires as an input expert evaluation of the criteria and individual locations in the protected areas using the Analytical Hierarchical Process. The presented method proved to be a feasible framework and a basis for evaluation of wetland values. The obtained results of the analysis showed overall similarities and important differences between these two observed wetlands and the 10 representative sites examined in detail. The analysis successfully identified locations and features of wetlands that require action for maintaining or increasing their overall value and function. The results can be used to identify locations and functions of wetlands that require conservational or other organizational improvements, and thus give valuable guidelines for decision makers. Further analysis using the presented model, with detailed local data and inclusion of other wetland areas, will contribute to the advancement of wetland research in the wider region of Southeastern and Central Europe, which was not sufficiently represented in previous studies.