Navotas and Malabon used to be one place. According to legend, the two surrounding seas ate away a narrow strip of Malabon until they created an opening connecting the two bodies of water. People in the area renamed the strip "butas" or "hole," which eventually evolved into the name Navotas. Other accounts indicate Navotas was named after its patron saint, San Jose de Navotas.
The history of Navotas involves its separation from Malabon. A movement to achieve this began on December 20, 1827, but it was not until more than 30 years later, on February 16, 1859, that the barrios of San Jose, Navotas and
Bangculasi were separated from Malabon. Later that year, on June 11, the new parish and municipality of Navotas became an independent town under the supervision of Friar Matias Navoa. In 1904, the town again merged with Malabon, and Bernardo Dagala, a native of Navotas, was elected municipal president.
On January 16, 1906, Navotas became an independent municipality with the enactment of Act. No. 1442, which separated it from Malabon. Navotas was officially founded as a city on June 24, 2007.