We study the spectral properties of infinite rectangular quantum graphs in the presence of a magnetic field. We study how these properties are affected when three-dimensionality is considered, in particular, the chaological properties. We then establish the quantization of the Hall transverse conductivity for these systems. This quantization is obtained by relating the transverse conductivity to topological invariants. The different integer values of the Hall conductivity are explicitly computed for an anisotropic diffusion system which leads to fractal phase diagrams.