At River Junction (MP 285.0), the line southward to La Crescent heads off on the west side. This is the ex-IMRL ex-Milwaukee line south and then southwest to Kansas City, and together with the line from the west end of the bridge forms a large wye. The main line proceeds south-southeast along the river, until it meets a line coming east from the wye at La Crescent at Bridge Switch (MP 283.6), where it turns east. The Mississippi River crossing from La Crescent to La Crosse comprises several separate bridges, with islands separating them. The westerly span is several girder bridge segments, while the easterly bridge includes a through-truss swinging span, with the remainder being simple girder bridge segments.
On the east side of the river, in Wisconsin, the single track, CTC, line passes Black River Drawbridge and West Wye Switch (MP 282.1), where a line once headed south from a wye junction, and turns northeast into La Crosse (MP 281.2), where the depot is on the south side of the tracks and the yard on the north side, passes under an overbridge carrying the erstwhile CB&Q passenger line through La Crosse and across the flat crossings with the stub of a UP (former C&NW) line into La Crosse, and then the BNSF freight line, both at Grand Crossing (MP 280.0), and turns north-northeast at the 14,906 ft. siding at Medary (MP 278.0), where that UP line (serving as that siding?) trails in on the north side, and there is a wye with a spur north to La Crosse Industrial Park. UP has trackage rights over the CP as far as Tunnel City, replacing a C&NW line that once ran along the south side of the Milwaukee Road line that is now the CP.
The extant line, with speed limits 79-60-50, turns east at West Salem, passes a detector at MP 269.0 and the 13,803 ft. siding at Bangor, turns north-northeast past Rockland, and northeast to the start of Double Track, CTC, at Sparta (MP 255.5) and detectors at MP 254.0, and turns east past Camp McCoy (MP 249.6) and Foresman, jogs northeast past the end of DT at Raymore (MP 246.3), and east again through Wisconsin's only tunnel to Tunnel City (MP 243.8), where the UP Winona subdivision continues due east and the CP line turns east-southeast, passing through Tomah (MP 240.1), where the platform is on the south side, a small yard on the north side, and a line once headed northeast to Wisconsin Rapids, the 13,619 ft. siding at Monroe (MP 237.0), Oakdale, a detector at MP 231.3, and the 14,685 ft. siding at Camp Douglas (MP 226.0), where a C&NW line once crossed on the flat.
The line turns southeast at New Lisbon (MP 221.2), where the present day line from Wisconsin Rapids joins from the north-northeast at a wye, and passes Mauston, the 12,000 ft. siding at Mile Creek (MP 211.0), a detector at MP 207.5, Lyndon, and the 9,400 ft. siding at Kilbourn (MP 199.0) before bridging over the Wisconsin River through the Wisconsin Dells scenic area. There is a platform on the north side of the track at Wisconsin Dells, but no obvious depot, although sources say one still existed in 2001. After running along the northeast side of the Wisconsin River for a couple of miles, the line turns east, and then east-southeast, as the river turns away to run parallel, but somewhat further south, with the line passing the 16,000 ft. siding at Lewiston (MP 189.0) and a detector at MP 183.0, to the 31,308 ft. siding at Portage (MP 178.2).
Portage has a platform and shelter on the south side of the tracks, but the depot is occupied by CP and is unavailable to Amtrak passengers. There is a freight yard across the tracks from the station, and a small storage yard just west of the station on the south side.