Mileposts are from Barstow via the erstwhile Santa Fe line through San Bernardino, Pasadena, and Los Angeles.
South of San Clemente, with bluffs to the east, and beach to the west, the single track, CTC, line passes a footpath crossing just north of the ownership change from Metrolink to San Diego Northern at County Line (MP 207.4), where the speed limit is 75 mph for passenger trains and 55 mph for freights and the line's direction turns from south-southeast to east-southeast, still running along the coast as the bluffs fall away, MP 208, a short stretch where the line is not directly adjacent to the beach before returning to it, a bridge over a stream, and a bridge over a road to the beach, part of San Onofre State Beach/Park to the west and I-5 to the east, the start of a short stretch of Two Main Tracks and a 4,480 ft. siding at CP Songs (MP 209.2), where the passenger speed limit rises to 90 mph, where the line is headed southeast along the coast, a spur into the power station, to the west, a road bridge overhead, I-5 still to the east, the San Onofre Nuclear Power Station to the west, with a street between it and the line, the end of the siding and return to single track, CTC, at CP San Onofre (MP 210.2), and more of San Onofre State Beach/Park to the west, with I-5 still to the east, and then runs through the large US Marine Corps base of Camp Pendleton.
Even in the 2000s, Camp Pendleton provides a welcome area of open countryside along the inland side of the line, past a detector at MP 210.3, Intermediate Signals at MP 211.x, Intermediate Signals at MP 215.2, Agra, dual highway bridges overhead carrying I-5 to the west side of the line, a bridge over drainage, a bridge over a road, Las Flores, the start of Two Main Tracks at CP Pulgas (MP 218.1), a pedestrian bridge overhead, Intermediate Signals at MP 220.x, two road bridges overhead, and Intermediate Signals at MP 221.x.
At the south end of Camp Pendleton, the line reaches a four-track yard between CP Stuart (MP 221.9) on the west track only, the six-track with building Stuart Mesa Maintenance Facility (MP 222.3), on the west side of the line, the end of the facility at CP Mesa (MP 222.6), also on the west track only, a bridge carrying the I-5 northbound lanes overhead, the end of Two Main Tracks at CP Fuller (MP 222.8), a bridge over the San Luis Rey River with I-5 bridges over that river to either side of the rail line, the start of a short stretch of Two Main Tracks at CP West Brook (MP 223.6), the southbound lanes of I-5 bridging overhead so that all of I-5 is to the east, a road bridge overhead, MP 225, a road bridge overhead, and the return to single track at CP East Brook (MP 225.3), once known as Fallbrook Junction, where the original line from San Bernardino through Temecula Canyon once trailed in on the east side.
The line turns south, past a street and harbor beyond it, alongside to the west, a bridge over the San Luis Rey River, the street to the west turning away, a grade crossing, a short stretch of restricted speed to 55-45 at CP Shell (MP 225.9), start of a 5,816 ft. siding, and then south-southeast, past a grade crossing, just north of the passenger station at Oceanside (MP 226.4), joint terminal point for Metrolink services from Los Angeles and Coaster services from San Diego, where Amtrak trains also stop, with two side platforms, an east side depot, and two stub platforms on the east side, south of the depot, for the DMU service to Escondido, on separate tracks that turn away east at the junction, where speed limits are back to 90-55, a signal bridge overhead, and the junction with the line east to Escondido at CP Escondido Junction (MP 227.2).
The main line continues parallel to the coast, past a grade crossing, an embankment, a bridge over Loma Alta Creek, a cutting a grade crossing, a bridge over Buena Vista Lagoon to the east and west, a road bridge overhead, the Coaster station with east-side platform at Carlsbad Village (MP 229.2), two grade crossings, MP 230, a grade crossing, a deck girder bridge over Agua Hedionda Lagoon, the Encina power station to the west at MP 231, a grade crossing to the power station, the start of Two Main Tracks at CP Farr (MP 231.4), a spur from the power station trailing in on the west side, a grade crossing, MP 232, a road bridge overhead, the Coaster station with two side platforms at Poinsettia (MP 233.3), two road bridges overhead, the return to single track at CP Ponto (MP 234.5), a deck girder bridge over Batiquitos Lagoon, a divided street alongside to the west, two grade crossings, a bridge over Encinitas Boulevard, the Coaster station with west-side platform at Encinitas (MP 237.7), where the passenger speed limit is 80 mph, a street alongside to the west with the beach to the west of it, and a grade crossing.
Two Main Tracks start again at CP Swami (MP 238.0), where the passenger speed limit is 70 mph, and return to single track at CP Cardiff (MP 239.7), past an embankment through San Elijo Lagoon, the start of another stretch of Two Main Tracks at CP Craven (MP 241.1), where the freight speed limit drops to 50 mph, a footbridge overhead, the Coaster and Amtrak station at Solano Beach (MP 241.8), with its impressive new station building to the east and two side platforms, the return to single track at CP Valley (MP 242.2), where the speed limit is back to 90-55, a road bridge overhead, an embankment over a marsh, a deck girder bridge over the San Dieguito River, the 2,675 ft. siding from CP Crosby (MP 243.3), past a road bridge overhead and a street alongside to the west, to CP Del Mar (MP 243.9), where the passenger speed limit has fallen to 65 mph, a grade crossing, and the former passenger station at Del Mar (MP 244.0), on a bluff above the beach, where trains used to deliver huge masses of patrons for the Del Mar Racetrack.
There is a road bridge overhead (County Road S21), a bridge over a street to a campground at Torrey Pines State Beach, and a deck girder bridge over Los Penasquitos Lagoon, before the line turns away from the ocean to head southeast, with bluffs to the west, past a bridge over a stream, CP Torrey (MP 248.8), where the passenger speed limit is back to 90 mph and a 4,632 ft. west side siding starts, the Coaster station with two side platforms at Sorrento Valley (MP 249.0), dual freeway bridges overhead, a grade crossing right at the bridges, and CP Pines (MP 249.8), end of the siding, where the speed limit is 50-20, turning east and then climbing very curvily southeast, with a street alongside to the northeast and bluffs alongside to the southwest, past dual road bridges high overhead, a street bridge high overhead, an embankment over drainage below, and then on a ledge above a gulley to the northeast, past a detector at MP 250.6, Intermediate Signals at MP 251.2, a detector at MP 251.7, and a detector at MP 252.2, and then between bluffs on both sides, past a detector at MP 252.8, dual road bridges overhead carrying Miramar Road, and the start of Two Main Tracks as the line turns south at CP Cumbres (MP 252.9), where the freight speed limit has risen to 50 mph, to a summit near Miramar Road (MP 253.0), where a spur from Miramar Naval Air Station trails in.
The line turns west-southwest, past dual road bridges overhead, Intermediate Signals at MP 253.2, MP 255, a bridge over drainage, a road bridge overhead, and Intermediate Signals at MP 256.4, and descends through Rose Canyon into urban San Diego, passing the return to single track at CP Elvira (MP 257.9), where the speed limit is 35-30, and a bridge over a street below (Balboa Avenue), and turning south-southeast, at the bottom of the grade, past I-5 alongside to the west and the start of Two Main Tracks at CP Morena (MP 260.5), where the speed limit is 75-55.
The line passes Pacific Beach, Mission Bay on the west side, a road bridge overhead, a street alongside to the east, I-5 alongside to the west, Morena, where it turns south, a bridge over drainage, dual road bridges overhead, the return to single track at CP Tecolote (MP 263.2), a bridge over a road below, Cudahy, where it turns just east of due south, a bridge over the San Diego River, I-8 triple bridges overhead, the facilities of General Dynamics on the west side, the start of Two Main Tracks at CP Friar (MP 264.1), the arrival of the San Diego Trolley's line on the east side, a grade crossing just north of the Coaster and Trolley station at San Diego’s Old Town (MP 264.2), where the speed limit is 60-40, with one west wide platform, two main line tracks, an island platform, two Trolley tracks, and an east side platform with depot, and a passenger subway under the tracks, and dual I-5 road bridges overhead.
Turning southeast, the line passes Washington Street, the former location of a wye on the west side to a Marine Corps depot, where the Trolley's Washington Street station is on the east side, and just east of due south past the Trolley's Middletown/Palm station on the east side, as the Trolley line runs east of the main line, rising to cross some streets and falling to pass below others, all of which the main line crosses at grade.
The three-track wide line turns south at CP Ash (MP 267.2), the end of CTC in favor of Yard Limits, and expansion to Four Main Tracks, past a grade crossing, and then at least one more grade crossing, before reaching the bayside station (four tracks with two side and one island platform, to the west, and depot on the east side, with the San Diego Trolley's line and platforms in between) in San Diego (MP 267.5) itself, where the speed limit is 15-10 and Amtrak and Coaster services end, with the westernmost pair of tracks reducing to one and three tracks crossing Broadway at grade, with two different trolley tracks just to their east, joining with the pair of main line tracks, and reaching Restricted Limits at Broadway (MP 267.7), where the passenger speed limit falls to 10 mph and ownership changes to BNSF, and turns southeast, with the Trolley line alongside to the east of the remaining main line track and eventually turning away east, to the San Diego Trolley yard at MTDB Yard (MP 268.8), where the San Diego & Imperial Valley and San Diego Trolley lines (using the same tracks at different times of day) to San Ysidro start.