At St. Croix Junction (MP CP 392.1/BNSF 410.5), where the joint trackage ends, the BNSF turns away to the east, and the CP turns south, as single track, CTC, to cross the river into Hastings. (MP 391.1), where a spur to Con Agra continues to the south and the main line turns southeast, expanding to 2MT, CTC, with speed limit 79-60-50, following the alignment of the river, but now on its west bank, and passing East Hastings (MP 388.7). The line reduces to single track at Vermillion (MP 385.9, where a former Milwaukee Road alignment headed south, and the present alignment continues southeast past the 10,473 ft. siding at Blackbird (MP 384.0), Stroms, a detector at MP 378.8, and the 18,376 ft. siding at Duke (MP 374.2), where the former alignment rejoins and the line turns east to come right alongside the river and into Red Wing (MP 370.7), where the depot is on the south side of the tracks and the yard on the north side.
The line turns east-southeast, a bit away from the river, past Wacouta, south and then east past the 12,441 ft. siding at Frontenac (MP 362.0), south-southeast alongside the river past a detector at MP 357.1 and a yard at Lake City (MP 353.8), southeast to the 12,360 ft. siding at Lakeview (MP 351.0), east past Reads Landing and southeast past the yard at Wabasha (MP 341.2), where the line leaves the river, turning south-southeast to the 13,326 ft. siding at Midland Junction (MP 338.0), where a Milwaukee Road line once headed west to Mankato,, south past a detector at MP 331.5, and south-southeast past the 11,736 ft. siding at Weaver (MP 325.0), where the river bank is regained. The line turns east to Minneiska, and southeast, along the river to the 11,556 ft. siding at Minnesota City (MP 316.0).
The DM&E (former Milwaukee transcontinental line) departs to the west at Minnesota City, having run parallel (on the west side) to the CP main line northward from Winona Junction (MP 312.2). The main line turns east-southeast and passes CK Tower (MP 310.1), at the north end of Winona, where a former C&NW line departs eastward, Winona (MP 308.2), where the depot is on the north side of the tracks and the yard on the south side, the 13,514 ft. siding at Homer (MP 303.0), a detector at MP 299.2) and Lemoille, and turns southeast past the 11,360 ft. siding at Donehower (MP 293.0), and south-southeast past Dakota and Dresback to River Junction West (MP 288.0).
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.