The detection and evaluation of flood damage in rural zones are of great importance for farmers, local authorities, and insurance companies. To this end, the paper proposes an efficient system based on five neural networks to assess the degree of flooding and the remaining vegetation. After a previous analysis the following neural networks were selected as primary classifiers: you only look once network (YOLO), generative adversarial network (GAN), AlexNet, LeNet, and residual network (ResNet). Their outputs were connected in a decision fusion scheme, as a new convolutional layer, considering two sets of components: (a) the weights, corresponding to the proven accuracy of the primary neural networks in the validation phase, and (b) the probabilities generated by the neural networks as primary classification results in the operational (testing) phase. Thus, a subjective behavior (individual interpretation of single neural networks) was transformed into a more objective behavior (interpretation based on fusion of information). The images, difficult to be segmented, were obtained from an unmanned aerial vehicle photogrammetry flight after a moderate flood in a rural region of Romania and make up our database. For segmentation and evaluation of the flooded zones and vegetation, the images were first decomposed in patches and, after classification the resulting marked patches were re-composed in segmented images. From the performance analysis point of view, better results were obtained with the proposed system than the neural networks taken separately and with respect to some works from the references.