Throughout the latter decades of the 19th century, orchards continued to spring up in the Delta's flood plains, interspersed with fields supporting other crops. At harvest time, farmers would set out the harvested goods at individual landings along the Sacramento River or its many tributary sloughs. From these, a river steamer would transport the goods to Sacramento, Stockton, or San Francisco, where local markets or long-distance transportation awaited.
If the goods were intended for an eastern market, they would soon be loaded aboard a Central Pacific or Southern Pacific train in this pre-Panama Canal era. (There really was no alternative for perishables, although grains could be shipped overseas without risk of spoilage.) By 1900, however, the Atchison, Topeka & Santa Fe Railway had invaded the territory of "The Octopus," completing its San Francisco & San Joaquin Valley subsidiary along the southern edge of the Delta region, from Stockton to Point Richmond. Santa Fe's stern-wheeler Frances would ply the rivers and sloughs, loading agricultural products for a shorter trip to the rail connection near Antioch.
The SP responded by incorporating a new railroad: the Sacramento Southern. Totally owned, funded, and operated by SP, the standard-gauge line was to be built in a southeasterly direction from Sacramento to Stockton. Plans called for the railroad to be 100 miles long, to serve as a common carrier for both freight and passengers, and to have two branches one running from Walnut Grove to the vicinity of Antioch, the other connecting Woodbridge with the SP main line. Although the Sacramento Southern never became more than a branch "feeder" line, SP had its reasons for these plans. At the time, the railroad was seeking an alternate passenger route from Sacramento to San Francisco Bay; its main line to Benicia was sinking into the Suisun Bay marshlands, and the SP was unsure it could control the problem.
In September 1907, the city of Sacramento granted the Sacramento Southern a franchise to build south from "N" Street with the stipulation that the waterfront levee be raised along the warehouse district, for the first several blocks of the line. Not only did the railroad agree to this, it also went on to elevate much of the right-of-way further south along the river. A large number of road crossings could thus be grade-separated, and train speeds raised accordingly. In keeping with Sacramento Southern's mainline ambitions, a substantial through-truss bridge over Riverside Avenue carried two tracks. By June 20, 1909, service began to Freeport, while construction crews continued to push southward. The line was surveyed and right-of-way purchased following the winding Sacramento River from Hood to Walnut Grove, but a shorter, more direct route was ultimately constructed bypassing Courtland.
Completion of the pivot bridge at Snodgrass Slough (with room for two tracks, although only one was ever laid) allowed through service to begin between Sacramento and Walnut Grove on March 12, 1912. Just one month earlier, the properties and assets of the nearly 25-mile long line were sold to the Central Pacific Railway as part of an SP corporate reorganization; the company's Suisun Bay marshland tracks had been stabilized, so the Sacramento Southern's mainline ambitions would never be realized. From this time forward the route would be popularly known by its timetable designation: the Walnut Grove Branch Line.
Self-propelled McKeen Motor Car railcars-with their distinctive round "porthole"-style window-provided passenger and freight service two times daily in each direction from Sacramento, supplemented by a single, steam-powered roundtrip freight run operating from Walnut Grove. In 1924, service was reduced to a single steam-powered "mixed" (freight and passenger) round trip (no more motorcars) operating from Sacramento. Over the next few years, however, rail competition increased in the area as the Western Pacific and its subsidiary Sacramento Northern built branches into the Delta.
Southern Pacific responded by extending its Walnut Grove branch another 7.5 miles south to Isleton; this extension which crossed Georgiana Slough on a Bascule lift bridge opened in late October 1929. In 1931, a three-mile spur was built to the Golden State Asparagus Company cannery on the Mokelumne River. With the Depression in full swing by this time, SP ceased carrying passengers on the branch the next year. Freight business continued briskly throughout the 1930s and 1940s.