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, past three road bridges overhead, a street alongside to the east, and MP 284, until it meets a line coming east from the wye at La Crescent at Bridge Switch (MP 283.6), where it turns east, past a dirt road grade crossing and a dirt road below on the west bank. The Mississippi River crossing from La Crescent to La Crosse comprises several separate multi-span bridges, with islands separating them. The westerly span is several girder bridge segments, of which the second is through girder, while the easterly bridge over the Mississippi includes a through-truss swinging span as its most easterly span, with the remainder being simple girder bridge segments, and the third bridge, over the Black River, is all through girder spans.
On the east side of the main river, in Wisconsin, the single track, CTC, line, with speed limits 79 mph for passenger trains, 60 mph for intermodal trains, and 50 mph for freights, passes a spur trailing in on the north side, a grade crossing, Black River Drawbridge and West Wye Switch (MP 282.1), where a line once headed south from a wye junction, extra track on the north side (a siding or second main track), at the same place as the west leg of the wye, MP 281, and a road bridge overhead, and turns northeast, past a road bridge overhead, into La Crosse (MP 281.2), where the two-storey brick depot is on the south side of the tracks and the yard on the north side, passes two grade crossings of streets with an intersection just to the south, seven yard tracks on the north side, east of the grade crossings, a road bridge overhead, ten yard tracks on the north side, a road bridge overhead, the erstwhile location of an overbridge carrying the erstwhile CB&Q passenger line through La Crosse, the east end of the yard running directly into a northwest quadrant connector, and the flat crossings with the stub of a UP (former C&NW) line into La Crosse, and then the BNSF freight line, with that northwest quadrant connector, both at Grand Crossing (MP 280.0), and turns north-northeast at the 14,906 ft. north side siding (25 mph on the siding) at Medary (MP 278.0), where that UP line (serving as that siding?) trails in on the north side, with a through girder bridge over a stream, a grade crossing, dual road bridges overhead, a footbridge overhead, and a bridge over a stream, all within the siding, a through girder bridge over a marsh or pond, and 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 dual road bridges overhead, an embankment, a road bridge overhead, a grade crossing, a street to the north in the town, two grade crossings, grain silos to the north, with two spurs on the north side, a detector at MP 269.0, two dirt road grade crossings, the 13,803 ft. north side siding (25 mph on the siding) at Bangor, with four grade crossings in town, within the siding, the end of one siding and start of another, a road to the north, and a spur to a lumber yard to the north, within the siding, and a grade crossing, turns north-northeast past a road briefly to the north, Rockland, and a grade crossing at 10th Avenue (MP 266.31), and northeast, past a bridge over a stream, to the start (40 mph on the turnout) of Double Track, CTC, at Sparta (MP 255.5).
There are three tracks for a gravel/cement plant to the north, a road bridge overhead, the tracks separate, a grade crossing, the tracks come back together, a grade crossing, an angled road bridge overhead, extra track to the north with a road alongside, a grade crossing, crossovers, a dirt road to the north, two grade crossings, and detectors at MP 254.0, and the line turns east past an acute angled through truss bridge overhead, a grade crossing, Intermediate Signal, Camp McCoy (MP 249.6), a grade crossing, a line separating on the north side, a grade crossing, Intermediate Signals, Foresman, and a bridge over a dirt road, and jogs northeast past a dirt road grade crossing, the end of DT (40 mph on the turnout) at Raymore (MP 246.3), an embankment, a wooded area, a dirt road to the north, and a road bridge overhead, and east again through a cutting and Wisconsin's only tunnel. to Tunnel City (MP 243.8), with speed limits 65/60/50 through the tunnel, where the UP Winona subdivision continues due east, on the north side.
The CP line turns east-southeast, passing a grade crossing in Tunnel City, a dirt track grade crossing, a bridge over a road, a dirt road grade crossing, a grade crossing, Tomah (MP 240.1), where the platform and stucco depot is on the south side, a small (four-track) yard on the north side, and a line once headed northeast to Wisconsin Rapids, a grade crossing east of the depot, a grade crossing, extra track on the north side, trailing in, the 13,619 ft. north side siding at Monroe (MP 237.0), with dual road bridges carrying I-90 overhead within the siding, a turn more northerly, a road bridge overhead, two bridges over drainage, extra track on the north side at Oakdale, a bridge over drainage, a grade crossing, Intermediate Signals, a bridge over drainage, a detector at MP 231.3, a grade crossing for County Road W, a bridge over drainage, a road bridge overhead, a spur trailing in on the north side, a grade crossing, and the 14,685 ft. north side siding at Camp Douglas (MP 226.0), with a road alongside to the north, a grade crossing, and a bridge over a stream within the siding, where a C&NW line once crossed on the flat, three dirt track grade crossings, a grade crossing, and a dirt track grade crossing.
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 a dirt road adjacent to the north, a dirt track grade crossing, a grade crossing, woods and fields, Intermediate Signals, two grade crossings, a bridge over a stream, a dirt road grade crossing, a grade crossing, a road alongside to the north, eight grade crossings in Mauston, a bridge over a stream, a grade crossing, a dirt track grade crossing, the 12,000 ft. north side siding (25 mph on the siding) at Mile Creek (MP 211.0), with a grade crossing in the siding, a dirt road grade crossing, extra track on the north side, a grade crossing, a detector at MP 207.5, a grade crossing, a dirt track grade crossing, a grade crossing, a dirt track grade crossing, a dirt road grade crossing, two grade crossings in Lyndon, a grade crossing, a dirt road grade crossing, a dirt track grade crossing in the woods, a grade crossing, the 9,400 ft. north side siding (25 mph on the siding) at Kilbourn (MP 199.0), dual road bridges overhead, a grade crossing, a park with a miniature railway to the east, and a bridge over a road, before bridging over the Wisconsin River on a deck girder bridge through the Wisconsin Dells scenic area, with a bridge over a street on the east side of the river.
There is a platform on the north side of the track at Wisconsin Dells (MP 195.1), with a brick depot on the north side also. After running along the northeast side of the Wisconsin River for a couple of miles, past a grade crossing in the woods, the line turns east, and then east-southeast, past another grade crossing, as the river turns away to run parallel, but somewhat further south, with the line passing a spur on the north side, a grade crossing, the 16,000 ft. north side siding (25 mph on the siding) at Lewiston (MP 189.0), with a bridge over a stream and a bridge over drainage within the siding, a road alongside to the north, a grade crossing, brush alongside to the north, a grade crossing, a bridge over a stream, a detector at MP 183.0, a dirt track grade crossing, extra track on the north side, and a grade crossing, to the 31,308 ft. north side siding at Portage (MP 178.2), with extra track to a facility on the north side, dual road bridges overhead, the extra track trailing in, a road bridge overhead, and a lake on the north side, all west of the station.
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 ten track freight yard across the tracks from the station, and a small storage yard just west of the station on the south side.