Fill taken from tunnel excavation and cuts was used to build a new railyard at Visitacion.
One of the cuts, at Visitacion Point, was 95 feet (29 m) deep and removed 750,000 cubic yards (570,000 m³) of material.
SP purchased Visitacon Cove and constructed 2.5 miles (4.0 km) of trestles to dump fill into San Francisco Bay, reclaiming 156 acres (63 ha) of land in total.
In total, more than 3,000,000 cubic yards (2,300,000 m³) of fill were used to reclaim land for the railyard, including 1,895,000 cubic yards (1,449,000 m³) of mud dredged from San Francisco Bay.
Because the Bayshore Yard was built on reclaimed land, building foundations were built on piles set, on average, 55 feet (17 m) deep, and the fill under the rails required constant replenishment for ten years until it was sufficiently compacted.

The Bayshore Yard contained approximately 50–65 miles (80–105 km) of track, in an approximately triangular area bounded by the Bayshore Cutoff main line (on the east), the Bayshore Highway (on the west, now Bayshore Boulevard), Tunnel 4 (on the north), and the deep cut at Visitacion Point (on the south).
It extended 8,400 feet (2,600 m) in length, measured north to south, and 1,800 feet (550 m) wide east to west at the apex of the triangle.
An additional 18.2 miles (29.3 km) of track were authorized in January 1917 along with the main shop buildings.
By 1921, the Bayshore Yard was substantially complete.

The design of the Bayshore Yard had thirty-eight tracks in the main freight space; seven tracks on both the north and south ends each had a capacity of fifty cars.
The north end of the yard also had fourteen storage tracks (total capacity of 472 cars) and eighteen classification tracks.
In all, the total capacity of the railyard was 1,068 cars on 24 inbound tracks, and 1,078 cars on 19 outbound tracks.
7 of the outbound tracks had a maximum capacity of 74 cars each.
Most of the tracks were spaced at 13 feet (4.0 m) between centerlines.
SP consolidated its freight and maintenance operations at the Bayshore Yard; maintenance had previously been performed at two locations: 16th and Harrison, and Mariposa.
The yard hump was the second hump constructed on the West Coast (after the classification yard at Roseville).

Steam locomotive maintenance would start in the Roundhouse.
Once the locomotive left the Roundhouse, it would move to the Transfer Pit (northwest of the Roundhouse), then be moved sideways on a 78-foot (24 m) long transfer table riding on six rails to line up with a track into the Erecting and Machine Shops, where a gantry crane would pick up the boiler and put it on a railcar to move it 300 feet (91 m) south to the Tank and Boiler Shop for refurbishment.
At the height of operations between 1911 and 1958, more than 3,000 were employed at the railyard and shops.
The railyard was handling 42,000 cars per month in 1921, and had 1,196 employees earning a monthly average of US$164.31 (equivalent to $2,400 in 2019).
As SP's most heavily traveled segment, the railyard handled 22 million gross tons per mile of freight in the 1920s and 46.5 million gross tons per mile during World War II.

The Bayshore Yard site was acquired by Tuntex (now Universal Paragon) in 1989.
Universal Paragon has proposed redeveloping the area as the Brisbane Baylands development.
As of 2013, the only buildings left from the railyard are the Roundhouse (built c.1910, abandoned), the Tank and Boiler Shop (built c.1920, leased to Lazzari Fuel in 1963 and used as a charcoal warehouse), and the Visitacion Ice Manufacturing Plant (built 1924 for Pacific Fruit Express, currently leased to Machinery and Equipment, Inc.).
Fill taken from tunnel excavation and cuts was used to build a new railyard at Visitacion. One of the cuts, at Visitacion Point, was 95 feet (29 m) deep and removed 750,000 cubic yards (570,000 m³) of material. SP purchased Visitacon Cove and constructed 2.5 miles (4.0 km) of trestles to dump fill into San Francisco Bay, reclaiming 156 acres (63 ha) of land in total. In total, more than 3,000,000 cubic yards (2,300,000 m³) of fill were used to reclaim land for the railyard, including 1,895,000 cubic yards (1,449,000 m³) of mud dredged from San Francisco Bay. Because the Bayshore Yard was built on reclaimed land, building foundations were built on piles set, on average, 55 feet (17 m) deep, and the fill under the rails required constant replenishment for ten years until it was sufficiently compacted.
The Bayshore Yard contained approximately 50–65 miles (80–105 km) of track, in an approximately triangular area bounded by the Bayshore Cutoff main line (on the east), the Bayshore Highway (on the west, now Bayshore Boulevard), Tunnel 4 (on the north), and the deep cut at Visitacion Point (on the south). It extended 8,400 feet (2,600 m) in length, measured north to south, and 1,800 feet (550 m) wide east to west at the apex of the triangle. An additional 18.2 miles (29.3 km) of track were authorized in January 1917 along with the main shop buildings. By 1921, the Bayshore Yard was substantially complete.
The design of the Bayshore Yard had thirty-eight tracks in the main freight space; seven tracks on both the north and south ends each had a capacity of fifty cars. The north end of the yard also had fourteen storage tracks (total capacity of 472 cars) and eighteen classification tracks. In all, the total capacity of the railyard was 1,068 cars on 24 inbound tracks, and 1,078 cars on 19 outbound tracks. 7 of the outbound tracks had a maximum capacity of 74 cars each. Most of the tracks were spaced at 13 feet (4.0 m) between centerlines. SP consolidated its freight and maintenance operations at the Bayshore Yard; maintenance had previously been performed at two locations: 16th and Harrison, and Mariposa. The yard hump was the second hump constructed on the West Coast (after the classification yard at Roseville).
Steam locomotive maintenance would start in the Roundhouse. Once the locomotive left the Roundhouse, it would move to the Transfer Pit (northwest of the Roundhouse), then be moved sideways on a 78-foot (24 m) long transfer table riding on six rails to line up with a track into the Erecting and Machine Shops, where a gantry crane would pick up the boiler and put it on a railcar to move it 300 feet (91 m) south to the Tank and Boiler Shop for refurbishment. At the height of operations between 1911 and 1958, more than 3,000 were employed at the railyard and shops. The railyard was handling 42,000 cars per month in 1921, and had 1,196 employees earning a monthly average of US$164.31 (equivalent to $2,400 in 2019). As SP's most heavily traveled segment, the railyard handled 22 million gross tons per mile of freight in the 1920s and 46.5 million gross tons per mile during World War II.
The Bayshore Yard site was acquired by Tuntex (now Universal Paragon) in 1989. Universal Paragon has proposed redeveloping the area as the Brisbane Baylands development. As of 2013, the only buildings left from the railyard are the Roundhouse (built c.1910, abandoned), the Tank and Boiler Shop (built c.1920, leased to Lazzari Fuel in 1963 and used as a charcoal warehouse), and the Visitacion Ice Manufacturing Plant (built 1924 for Pacific Fruit Express, currently leased to Machinery and Equipment, Inc.).
Bayshore Cutoff