Township before entering Plumsted Township, where the road turns northwest and north through forested areas of the Fort Dix Military Reservation. After leaving the Fort Dix grounds, CR 539's speed limit drops to and enters a mix of farms and woods with a few homes and businesses, heading northwest and crossing CR 640. Following this junction, the route enters more wooded areas of residential development, passing New Egypt Speedway before crossing CR 528. The county route becomes concurrent with CR 528 Truck and passes more rural areas of homes before becoming Hornerstown Road and reaching an intersection with CR 537, where CR 528 Truck turns west onto that route. Upon crossing CR 537, CR 539 enters Upper Freehold Township in Monmouth County and intersects CR 27, at which point the road becomes Trenton-Forked River Road and heads through agricultural areas with some homes, crossing another section of CR 27. The route heads through more areas of farms, woods, and residences, where it turns west onto Davis-Allentown Road at a roundabout with CR 539 Alt. and runs northwest through more rural areas. CR 539 enters Allentown, where it becomes High Street and passes through residential areas before intersecting CR 524. CR 539 forms a concurrency with CR 524, with the two routes continuing northeast along Main Street to a short overlap with CR 526. The road leaves Allentown for Upper Freehold Township and enters farmland as it intersects CR 526 Spur. A short distance later, CR 524/CR 539 reaches an interchange with Interstate 195 (I-195). At this point, the name of the road becomes Old York Road and it forms the border between Robbinsville Township, Mercer County to the west and Upper Freehold Township, Monmouth County to the east briefly before CR 524 splits from CR 539 by turning east along New Canton-Stone Tavern Road. CR 539 continues northeast past a mix of farms and residential subdivisions before passing through more agricultural surroundings. The road briefly turns east and runs through a wooded part of Millstone Township, Monmouth County. After a turn to the north, CR 539 enters East Windsor Township in Mercer County and passes farms with some homes, intersecting CR 630 before passing over the New Jersey Turnpike (I-95). Following this, the road passes through residential subdivisions before entering Hightstown. CR 539 then becomes South Main Street at this point and passes homes, with CR 571 joining the route