At the moment, the theory, methods and techniques concerning the application of mathematical models are wide-used. Nevertheless such problems as a problem of multi-criteria models’ quality estimation, a problem of analysis and arrangement of models’ classes, a problem of justified selection of applied task-oriented models are not well investigated yet. The importance of the considered problem increases when the object of research is described not via a single model, but via a multiple-model complex, consisting of models related to different classes or combined models (for example, analytical-imitating, logical-algebraic, etc). Aforementioned problems are the primary objects of the theory of mathematical models’ and multiple-model complexes’ quality control. We proposed to implement this theory in the Information Fusion applied area. In the paper software prototype for Information Fusion quality estimation and models’ quality control in the sphere of operational river flood forecasting is proposed.