In 1869 the Central Pacific Railroad completed a rail line from Sacramento to San Francisco. The line ran through Stockton with a coaling station in Ellis at the foot of the Altamont Pass. Ellis was later moved a couple of miles east and became Tracy. The last leg of the journey to San Francisco was completed by ferry. Shortly after the line was completed, Lathrop Junction was developed and consisted of a roundhouse, railroad shop, yards and hotels for railroad employees.

With the driving of the golden spike at Promontory Point, Utah in May of 1869, the Central Pacific and Union Pacific railroads, completed the transcontinental railroad between Omaha, Nebraska and Sacramento, California. However there was still one point in the system where passengers and freight still has to use riverboats to cross the San Joaquin River at Mossdale. On September 8, 1869 the bridge over the San Joaquin river (see trestle in photographs) was completed and the first train crossed the bridge over the San Joaquin River. This was really the last link in the transcontinental railroad system.

Prior to becoming San Joaquin County's seventh incorporated city in 1989, Lathrop's identity and local governance centered around the Lathrop Water District, which provided public water to the community. Today Lathrop's government features a city hall at 16775 Howland Road, Suite #1 (209) 858-2357 with a full complement of municipal departments. The Lathrop Water District became the new city's Public Works department.

Due to flooding in the winter of 1982/83, which impacted several package wastewater treatment plants, the community was put under a building moratorium. The moratorium gave the community time to abandon the ineffective package plants and connect into the City of Manteca wastewater treatment plant. The City of Lathrop has the rights to 14.7% of all the sewer treatment plant capacity in the nearby Manteca wastewater treatment plant.

Today Lathrop has a population of 12,050 and is one of the fastest growing cities in San Joaquin County. In October of 1997 Lathrop annexed approximately 6,800 acres of land on the west side of Interstate 5 into the city limits. This area is planned as for development with several theme resorts, hotels, golf courses, commercial development and housing. This annexation known as the West Lathrop Specific Plan includes the River Islands and Mossdale Village projects. Mossdale Village will be the first project to get started and is expected to be under construction by the fall of 2003.

In addition to its continued use of Manteca's wastewater treatment plant, Lathrop also has it's own wastewater treatment plant in the Crossroads Business Park. The City of Lathrop is planning to build a new sewer treatment plant in the Crossroads project that will be operated by U.S. Filter to serve the new development on the west side of Interstate 5.