The effects of rail infrastructure on the connectivity of habitat for Chinook (Oncorhynchus tshawytscha), Coho (O. kisutch), Sockeye (O. nerka), Chum (O. keta), and Pink salmon (O. gorbuscha) and anadromous Rainbow Trout (O. mykiss) in British Columbia were estimated. Habitats upstream of major hydro dams lacking fishways were not considered. Natural habitat accessibility was modelled for each species based on swimming ability and stream gradient, excluding habitats upstream of steep gradients, large waterfalls, or areas with subsurface flows. Within these naturally accessible habitats, areas that may support spawning and rearing were identified using intrinsic potential models. Anthropogenic structures that may be barriers to fish movement were then overlaid to identify habitat that may be blocked. Similar estimates of lateral habitat fragmentation were made by modelling lateral habitat along the floodplain, overlaying rail-stream crossings and lines, and identifying areas that may be disconnected by them.