Mathematical models of motility are often based on random-walk descriptions of discrete individuals that can move according to certain rules. It is usually the case that large masses concentrated in small regions of space have a great impact on collective movement of the group. For this reason, many models in mathematical biology have incorporated crowding effects and managed to understand their implications. Here, we build on a previously developed framework for random walks on networks to show that in the continuum limit, the underlying stochastic process can be identified with a diffusion partial differential equation. The diffusion coefficient of the emerging equation is in general density-dependent, and can be directly related to the transition probabilities of the random walk. Moreover, the relaxation time of the stochastic process is directly linked to the diffusion coefficient and also to network structure, as it usually happens in the case of linear diffusion. As a specific example, we study the equivalent of a porous-medium type equation on networks, which can be coarse-grained to obtain a known nonlinear equation. These findings also provide insights into reaction-diffusion systems with general diffusion operators, which have appeared recently in some applications.