Low-salinity (LS) waterflooding has been a topic of substantial recent interest in the petroleum industry. Studies have shown that LS brine injection can increase oil production relative to high-salinity (HS) brine injection, but contradictory results have also been reported and a mechanistic explanation of these findings remains elusive. We have recently developed a pore-scale model of LS brine injection in uniformly wetted networks (Watson et al. in Transp Porous Med 118:201-223, 2017), and we extend this approach here to investigate the low-salinity effect (LSE) inheterogeneouslywetted media. We couple a steady-state fluid displacement model to an innovative tracer algorithm and track the evolving salinity front as oil and HS brine are displaced from the network. The wettability of the pore structure is locally modified where water salinity falls below a critical threshold, and simulations show that this can have significant consequences for oil recovery. Our results demonstrate that, for heterogeneously wetted networks, the oil-wet (OW) pores are the only viable source of incremental oil by LS brine injection. Moreover, we show that a LS-induced increase in the displaced OW pore fraction is a necessary, but not sufficient, condition to guarantee additional oil production. Simulations further suggest that the initial OW pore fraction, the average network connectivity and the initial HS brine saturation are factors that can determine the extent of incremental oil recovery following LS brine injection. This study clearly highlights that the mechanisms of the LSE can be markedly different in uniformly wetted and in non-uniformly wetted porous media.