W.F. Holt founded the community in 1903, initially calling it Holton — then settling on Holtville, apparently on the theory that a place named after yourself deserves at least two attempts at the name. Holt was a developer who understood that the Imperial Valley's future lay in irrigation, and he positioned the community accordingly. Swiss-German immigrants were among the early settlers who came to farm the desert land made arable by the new canal systems, bringing agricultural expertise and, eventually, a distinctive community character. Holtville incorporated on June 20, 1908, establishing itself as an independent city rather than a company town or unincorporated community. It has remained a small, close-knit agricultural city ever since.

Holtville bills itself as the Carrot Capital of the World, a designation it has defended with considerable enthusiasm since 1947 when the Imperial Valley Carrot Festival began — an annual celebration that has continued with only brief interruptions for decades. The Imperial Valley's climate and irrigation infrastructure make it well-suited to carrot production: the warm winters, reliable sunshine, and fertile soil produce carrots that are harvested and shipped across the country. The festival draws visitors with a carrot cook-off, parade, and carnival. It is the kind of local celebration that turns a single agricultural product into a community identity — and in Holtville's case, that identity has held for generations.

Two figures born in Holtville made their marks in very different fields. George E. Brown Jr. represented California in the US House of Representatives for decades, serving from 1963 to 1999 with a brief interruption, becoming one of the most influential voices on science and technology policy in Congress. His advocacy for research funding and environmental protection left a legacy well beyond the Imperial Valley. Daniel Everett came from a different world entirely: a linguist who went to the Amazon to work with the Pirahã people of Brazil and returned with findings that challenged foundational assumptions in linguistics — specifically, Noam Chomsky's theory that certain linguistic structures are universal to all human languages. Holtville produced a congressman and a revolutionary linguist. Not a bad return for a carrot town.

On March 2, 2021, a SUV carrying 25 people — mostly farmworkers — collided with a semi-truck at a railroad crossing near Holtville. Thirteen people died, making it one of the deadliest crashes in Imperial County history. The victims were largely undocumented migrants, and the tragedy drew national attention to the conditions facing agricultural workers in the valley: long distances traveled to reach fields, crowded transport, and the invisible labor that sustains American food production. Holtville, a city that had known itself as the Carrot Capital, suddenly had to hold a different kind of grief alongside its agricultural identity. The memorial that followed honored people whose names most of the country had never known.