A heterogeneous continuous time random walk is an analytical formalism for studying and modeling diffusion processes in heterogeneous structures on microscopic and macroscopic scales. In this paper we study both analytically and numerically the effects of spatio-temporal heterogeneities onto the diffusive dynamics on different types of networks. We investigate how the distribution of the first passage time is affected by the global topological network properties and heterogeneities in the distributions of the travel times. In particular, we analyze transport properties of random networks and define network measures based on the first-passage characteristics. The heterogeneous continuous time random walk framework has potential applications in biology, social and urban science, search of optimal transport properties, analysis of the effects of heterogeneities or bursts in transportation networks.