We present a Wigner function-based approach for the particle density evolution in fermionic and bosonic open quantum many-body systems, including the effects of dephasing. In particular, we focus on chains of non-interacting particles coupled to Lindblad baths. The dissipative processes, described by linear and quadratic jump operators, are modulated by inhomogeneous couplings. Following a semi-classical approach, we find the differential equation governing the Wigner function evolution, which can be solved in closed form in some particular cases. We check the accuracy of the Wigner approach in different scenarios (i.e. Gaussian jump frequencies), describing the density evolution and the transport phenomena in terms of classical quasi-particles.