At the crossovers at St. Croix Junction (MP CP 392.1/BNSF 410.5), where the joint trackage ends, the CP turns south, and the two-track BNSF turns away to the east, CTC, speed limit 60 mph, past Hastings, where the line turns just south of due east, Burns (MP 407.8), where the double track reduces to single track, CTC, a bridge over the St. Croix River from Minnesota into Wisconsin, Prescott (MP 407.7), where Double Track (current-of-traffic) begins, the line turns curvily southeast, along the east bank of the Mississippi River, and the CTC is replaced by Track Warrant Control, Automatic Block Signals, detectors at MP 405.0, a crossover at Diamond Bluff (MP 396.3), where the line leaves the river for a short distance, and detectors at Hager (MP 391.0), turning east, along the riverbank again, past crossovers at Bay City (MP 386.3), southeast, east, and a big curve around to the south, passing Maiden Rock (MP 378.7) in the process, as the river becomes Lake Pepin for twelve miles or so.
There are detectors at MP 372.7, a turn to the east-southeast, still following the riverbank (or lakeshore), past Stockholm and a crossover at Pepin (MP 366.2), where it turns just south of due east, past the start of single track, CTC, at Mears (MP 362.9), a bridge over the Chippewa River, a detector at MP 362.5, and the return of Double Track (current-of-traffic), TWC, ABS at Trevino (MP 362.1), where an erstwhile Milwaukee Road line once crossed and the line leaves the riverbank for a short distance, turning south-southeast at Nelson (MP 358.7), returning to the riverbank past a bridge over an inlet, crossovers at Alma (MP 351.3), where it turns south and then south-southeast, leaving the riverbank for some distance, past detectors at MP 345.0 and a crossover at Cochrane (MP 343.1), returning to the riverbank past a crossover at Fountain City (MP 333.9), past the start of single track, CTC, at Winona Junction (MP 328.2), where an erstwhile Chicago & Northwestern line once headed east, a detector at MP 327.5, additional track at Winona (MP 327.2), and a 10,145 ft. siding at East Winona (MP 325.7), where the former Green Bay & Western (Now CN) heads east-northeast, after which DT, TWC, ABS returns.
The line turns east-southeast, still following the riverbank, past a crossover at Trempeleau (MP 317.4), where that erstwhile C&NW line comes alongside to the north, turning southeast and away from the river past additional track at Lytle (MP 311.2), south-southeast, past detectors at MP 307.2, back to the riverbank, and south past the erstwhile C&NW route turning away and the end of the riverbank, the start of single track, CTC, at Sullivan (MP 303.1), the start of Yard Limits, ABS, at North La Crosse (MP 300.2), the yard on the west side, where an erstwhile CB&Q passenger line once headed southwest, and the flat crossing, with northwest quadrant connector, with the CP (former Milwaukee Road) at Grand Crossing (MP 299.9).