The area was part of the Carrum Carrum swamp an expansive wetlands ecosystem encompassing more than 11,000 acres between Mordialloc and Frankston.

In 1866, the first survey of Carrum Carrum swamp was carried out. Subsequently the land between Mordialloc Creek and Seaford was divided into 18 allotments and sold at auction.

In 1879, aiming to reclaim land for agriculture and housing, a 10-metre wide channel known as Patterson Cut was created to the sea. The channel widened during later floods and was renamed to Patterson River.

In 1918, 170 acres of pastoral land to the north and west of Patterson River were acquired, leading to the establishment of a dairy farm. Later, in 1926, the same owner developed a golf course and clubhouse on the property.

The Melbourne Metropolitan Board of Works became the Melbourne metropolitan drainage authority.

The Southern Hemisphere's first dry dock marina was founded at Patterson Lakes, originally known as Whaler's Cove Marina before being renamed to Patterson Lakes Marina. In 1966, the local coastguard branch and the Patterson Lakes Canoe Club were both established.

Work commenced on transforming 400 hectares of land along McCleod Road in Carrum, creating 23 kilometres of waterfront for residential properties. The developers designed the Tidal Waterways and Quiet Lakes for this new suburb.

Between 2002 and 2007 iconic Australian sitcom Kath & Kim was filmed at a property in Patterson Lakes. The house, which stood in the fictional suburb of Fountain Lakes on the show, was demolished in 2022.

Residents of Patterson Lakes have to reduce service levels and eliminate the Special Precept Rate that was formerly levied on all residents. Since 2014, only two paid direct services continue in Patterson Lakes, which are included on South East Water bills: the Jetty Infrastructure Charge and the Quiet Lakes Bore Flushing Charge.