In this paper, we combine deep learning concepts and some proper orthogonal decomposition (POD) model reduction methods for predicting flow in heterogeneous porous media. Nonlinear flow dynamics is studied, where the dynamics is regarded as a multi-layer network. The solution at the current time step is regarded as a multi-layer network of the solution at the initial time and input parameters. As for input, we consider various sources, which include source terms (well rates), permeability fields, and initial conditions. We consider the flow dynamics, where the solution is known at some locations and the data is integrated to the flow dynamics by modifying the reduced-order model. This approach allows modifying the reduced-order formulation of the problem. Because of the small problem size, limited observed data can be handled. We consider enriching the observed data using the computational data in deep learning networks. The basis functions of the global reduced order model are selected such that the degrees of freedom represent the solution at observation points. This way, we can avoid learning basis functions, which can also be done using neural networks. We present numerical results, where we consider channelized permeability fields, where the network is constructed for various channel configurations. Our numerical results show that one can achieve a good approximation using forward feed maps based on multi-layer networks.