The boundary between the lines south of Oakland and the line north of Oakland, where the mileposts increase in both directions, is at the ex-SP Desert Yard in Oakland (named because it had no water supply in steam days), MP 2.2, where the line to the former bayfront station at the Oakland Mole cuts off to head northwest into todayís intermodal rail-to-ship (and vice versa) transfer facilities. Todayís Desert Yard is oriented north-northeast, west of the new segment of freeway built to replace that several blocks further east that collapsed in the Loma Prieta earthquake (the one that stopped the World Series) in October 1989. Across the new I-880 freeway segment are the closed facilities of Oakland 16th Street Station, closed because the buildings were severely damaged in that same earthquake. In 2005, the buildings still stand, complete with the remnants of the streetcar/interurban platforms on the upper floor that had made the station, when opened in 1916, the very embodiment of an intermodal transportation center.
North of the former location of Oakland 16th Street station, connectors from the adjacent I-880 freeway to the San Francisco Bay Bridge climb to pass over the railroad (two bridges), followed by the Grand Avenue bridge overhead, two bridges carrying I-880 itself as it curves to the west side of the line, along with three bridges comprising I-580 and a connecting ramp. There is a Control Point at 26th Street (MP 3.2), on track 2 only, followed by crossovers at 34th Street (MP 3.7). The line turns to just west of due north as it passes under the many freeway ramps and the 40th Street bridge, and with I-80 and Shellmound Street now on its west side leaves Oakland and enters Emeryville, a small community sandwiched between Oakland, Berkeley, and the waters of the San Francisco Bay.
There are more crossovers and the connection from track two to the passenger tracks at West Emeryville (MP 4.5). Powell Street crosses over the line on a bridge between West Emeryville and Emeryville station. With the new Oakland Jack London Square station now on the far side of the Amtrak coach yards at West Oakland, Emeryville (MP 4.5) is the origination point for the transcontinental Amtrak trains, the California Zephyr, as well as the point at which San Francisco connecting passengers change from the buses that brought them across the bay bridge to the trains on the Capitol and San Joaquin routes, which originate further south. (The same arrangements also prevail in reverse.) Emeryville station is on the east side of the four track line (two of them are extra tracks to the west side), with two tracks devoted to passenger trains on the east side of the main freight lines at this location. There is a large concrete or stucco depot building, and a footbridge north of the depot that crosses the line to the parking lots to the west. The connection back into the main lines, and associated crossovers, is at East Emeryville, MP 4.7, where the total trackage reduces to two main tracks.
North of Emeryville, there are grade crossings at 65th, 66th and 67th Streets, SR 13 passes below an underbridge, there is a spur on the east side, an aquatic park on the west side between the line and I-80, along with more crossovers at Shellmound, MP 5.2, grade crossings at Bancroft Way and Addison Street before the two main track, CTC-controlled line reaches the Berkeley station, which has a smaller depot on the east side of the line at MP 6.2, and University Avenue bridges overhead. There are grade crossings at Hearst Avenue, Virginia Street, Cedar Street, Jones Street, Page Street, Camelia Street, Gilman Street, and Harrison Street, Buchanan Street bridges overhead, an on-ramp and then I-80 bridge overhead as that freeway crosses to the east side of the line and I-580 resumes on the west side of the line. The line curves gently to the northwest, with I-580 alongside to the west, Central Avenue bridges overhead, Meade Street bridges overhead, there is a wye on the west side of the line to the Richmond Pacific Railroad (the former connection to the Santa Fe, which still provides the connection through to the BNSF line allowing BNSF trains to reach Oakland wharf side trackage), and crossovers at Stege (MP 9.4) as Carlson Boulevard comes alongside to the east, adjacent to a grade crossing at Carlson Boulevard.
On the east side of the line, the BART line comes alongside, having followed the routing of the former Santa Fe Oakland Branch, as 23rd Street passes underneath. McDonald Avenue, a divided highway passes underneath. Richmond station, MP 12.0, is the only place where Amtrak has a direct connection with the BART heavy-rail rapid transit system. The station has an island platform with an umbrella shelter between the tracks, with passenger subway and station at ground level below. The BART station is immediately adjacent to the main-line station, on the east side of the main line, with the BART train storage sidings and maintenance depot immediately north of its station, as the line curves back to due north. Barrett Avenue passes underneath, and Pennsylvania Avenue or 13th Street bridges overhead.
A little further north, the BNSF route out of Richmond crosses overhead on a through girder bridge and then turns to run alongside to the east. There is another wye on the west side at MP 13.6, just north of the BNSF overbridge, connecting in a former-SP branch now run by Richmond Pacific Railroad from Richmond Transfer, Chesley Avenue and Market Avenue cross at grade, there are detectors at MP 14.1, the line bridges over Wildcat Creek, there are grade crossings at Brookside drive and Parr Boulevard, and crossovers at San Pablo (MP 15.3), where there are also yard tracks on the west side of the line as far as MP 17.1. Richmond Parkway crosses overhead, after which there is housing on the east side between the ex-SP line and the BNSF line, before that line again comes.alongside on the east, at a higher level than the former SP line, as a footbridge passes overhead. After coming momentarily alongside San Pablo Bay at the location UP calls Giant, MP 18.9, where there is a spur (adjacent to the location BNSF calls North Bay), the ex-SP line turns east and the BNSF east-northeast on the landward side of a promontory to run alongside the curving shore of the bay.
The ex-SP line turns northeast along the bay, and housing again intervenes between it and the BNSF line. The ex-SP line turns east along the shore of the bay to Pinole (MP 20.4), where there are crossovers, and the BNSF line is again alongside, but higher, on the landward side. The BNSF line heads away due east, while the ex-SP line turns northeast, passing a grade crossing at Tenment Avenue and crossing over Pinole Creek continuing to follow the shore of the bay (with housing developments on the landward side), through the crossovers at Hercules (MP 20.8), past Rodeo and past the former site of a once rail-connected oil refinery on the landward side (now a housing development), the Pacific Avenue road overbridge, and a still operational refinery on the southeast side of the line with loading docks on the northwest side at Oleum (MP 23.3), through a short tunnel (604ft.) at MP 23.7, and then past an oil refinery with fuel loading facilities for many tank cars, on the southeast side of the line, with spurs entering it, at Tormey (MP 24.1), and another spur at Selby (MP 24.5), followed by another short tunnel as the line turns east along the south shore of Carquinez Strait.
As the line passes under the Carquinez Strait (I-80) bridges high above (the old out-of-service bridge is suspension, the newer two cantilever style), it passes through the C&H Sugar refinery before reaching Crockett (MP 26.0), where the old depot remains on the south side of the line. There are crossovers at Costa (MP 27.5). At Port Costa the remnants of the former train ferry dock that once connected with Benicia before the Suisun Bay Bridge was built are still rotting at the water line. There are detectors at MP 27.8 and crossovers at Howard (MP 30.1) as the line turns south-southeast following the shore of the bay, and then turns east-southeast past the crossovers and five north side sidings at Ozol (MP 31.0), where a third track on the landward side begins (3MT, CTC). There are detectors at MP 31.3, as Embarcadero Street appears alongside to the north, and the line turns east, across the Berrellesa Street grade crossing, to the passenger station at Martinez Depot (MP 31.7), where there is an island platform as well as a south side platform in front of the 2000s brick depot building on the south side. The old depot building remains on the south side, on the east side of the Ferry Street road crossing at the east end of the new station, with former SP 0-6-0 1258 and a couple of cars stuffed-and-mounted in a small park on the north side of the line. East of the station, Marina Vista runs alongside to the south, the three tracks end at the crossovers at Ferry (MP 31.8), and the line towards Sacramento heads off to the south (east) side of the erstwhile Mococo line onwards to Tracy at Martinez (MP 32.0)
There is a stiff climb to the Suisun Bay Bridge alongside an oil refinery, which is connected to the Mococo line that diverged from the Cal-P just before the climb to the bridge began, during which the Cal-P line crosses above the Mococo line on the ground below, as the Cal-P line turns west-northwest, through the crossovers at Vista (MP 33.0), under the concrete bridge carrying the south end of the west span of I-680 and across the bridge (with its lifting span control point at MP 33.7), with the I-680 bridge alongside to the west (and the new one almost complete, in November 2006, alongside to the east). On the north side of Suisun Bay, the line turns northeast, passing beneath the north end of the new east span of I-680, with the two tracks at different heights momentarily, passing an automobile carrier yard on the south side, with a steel trestle over an access road to that facility, and another petrochemical facility on the north side, and the mothball fleet in Suisun Bay, both on the east side of the line at Benicia (MP 34.5), where the remnants of the line from the erstwhile Benicia ferry dock trail in on the east side (having run under the bridge).
The Cal-P line runs northeast through the fringes of the Sacramento Delta, past detectors at MP 37.1, through Bahia (MP 38.0), where the double-track remnants of the Benicia line trail in from the west there are three tracks for a short distance, and turns due north to pass around Grizzly Bay. There are crossovers at Cordelia (MP 42.3), with a bridge over a wetlands stream between them, where the line turns north-northeast, MP 43, a dirt road grade crossing, still in the wetlands, MP 44, and detectors at MP 45.1. The California Northern line from Napa Junction and Schellville joins from the west with a wye just before the line turns northeast past a grade crossing, and a Maintenance of Way yard on the south side, to reach the passenger station at Suisun-Fairfield (MP 48.9), where the depot is on the southeast side of the line. There is a road bridge overhead, two grade crossings, and crossovers at Tolenas (MP 52.0), where a spur to Travis Air Force Base goes off to the east. There are three rail-served industries on the south side, a grade crossing, a road parallels on the south side, and another grade crossing. A Sacramento Northern line to Fairfield and Vacaville once passed overhead on a through girder bridge (now removed) near Cordera, another Sacramento Northern line connects in from the southeast at Cannon, there is a grade crossing, a golf course on the south side, crossovers at Elmira (MP 59.4), where the SP branch to Vacaville and beyond once left to the west, a grade crossing, a road alongside to the south, a grade crossing, a spur trailing in on the south side, two grade crossings, two bridges over streams, Intermediate Signals at MP 61.x, a grade crossing, and a bridge over drainage..
There are Intermediate Signals and detectors at MP 63.2, three grade crossings, crossovers at Pitt (MP 65.5), a grade crossing, three closed grade crossings, two grade crossings in Dixon, Intermediate Signals at Dixon at MP 67.5, two grade crossings, a spur on the south side trailing in, two grade crossings, a rail-served industry on the south side with its spur trailing in, Intermediate Signals at MP 73.2, a dirt road grade crossing, a bridge over drainage, a grade crossing, the I-80 bridges overhead, and crossovers at West Davis (MP 75.0), where the west leg of the wye with the California Northern Line (former West Valley Line) to Tehama heads off to the north, and the Cal-P line turns east-northeast.
The striking passenger depot at Davis (MP 75.4) is in the middle of the wye, on the north side of the Cal-P, there is a bridge over a bike path, a bridge over a street, the east leg of the wye trails in, I-80 exits and entrance ramps alongside to the south, a road bridge overhead, I-80 alongside to the south, and the crossovers at East Davis (MP 75.6). There is a pedestrian bridge overhead (and across I-80)a bike path between the line and I-80, a road bridge overhead, detectors at MP 78.7, a grade crossing, a road between the line and I-80 on the south side, and a spur at Swingle (MP 79.1). The fields of the Sacramento Delta give way to a constructed flood control channel known as the Yolo Bypass, across which the Cal-P travels on a causeway from West Causeway (MP 81.1) to East Causeway (MP 85.2), where I-80 bridges overhead. There is a road bridge overhead, a flat crossing with the Yolo Shortline at Mikon (MP 86.9), as the line turns east, and a bridge over a road below. There is a connection with the same Yolo Short Line via a short spur trailing in to the south of the line at West Sacramento (MP 88.1), a bridge over a street and a grade crossing, after which the line crosses the Sacramento River on the I Street Bridge (MP 88.5) into Sacramento, which also carries a road overhead. There is an occasional flat crossing immediately east of the bridge used when needed to get locomotives and rolling stock into and out of the California State Railroad Museum on the south side of the line, with three concrete bridges carrying I-5 and a ramp overhead. There are crossovers at Sacramento (MP 88.8) between the occasional crossing and the station. From Sacramento to Roseville, where there is another vast marshalling yard and locomotive maintenance facilities, the line is again in an urban area.
There are two platforms with umbrella sheds, serving three through tracks at the Sacramento Depot (MP 88.9), where the major depot is on the south side of the line, with a terminal station on the light rail line just south of the main line platforms, and the former SP locomotive shops, now in the process of redevelopment, are on the north side. Immediately east of the station platforms, the line curves due north and then immediately due east again, bridging over a street. The tracks from the shops used to join the main line at the second curve, and there is still some residual trackage on the north side of the line at this point. The Sacramento light rail systemís north line passes underneath, on the east side of a street that also passes underneath, and the former location of a Sacramento Northern line crosses at grade. A road passes underneath, and then another one does. The Blue Diamond Almonds plant is on the south side and grain elevators to the north. At Haggin, once just the location of an SP overcrossing of the Western Pacificís main line below, there are now connections on the north side of the ex-SP line from both the west (at West Haggin, MP 90.2, from the north track only), curving around on the east side of the WP line, and east (at East Haggin, MP 90.6, where there are also crossovers) down to the ex-WP line facing north.