The name Kaipara reaches back to the 15th century and an act of culinary admiration. The Arawa chief Kahumatamomoe travelled to the harbour to visit his nephew at Pouto, on the sandy northern arm of the entrance. At the welcoming feast, he was so impressed by the cooked root of the para fern, the king fern, that he named the entire district Kai-para: food of the para. In te reo Maori, kai means food and para means king fern. The local iwi, Ngati Whatua, have maintained settlements and marae around the harbour's margins for hundreds of years, using its waterways as highways between communities. The harbour provided, and still provides, a ready means of moving between marae, its broad channels and sheltered inlets serving as a network of natural roads long before Europeans arrived.

James Cook sighted the harbour in 1770 during his first voyage and named it False Bay, noting in his journal that it had "the appearance of a Bay or inlet, but I believe it is only low land." He was wrong about that, but he was wise not to attempt the entrance. The first European shipwreck was the Aurora, a 550-ton barque, in 1840. The brigantine Sophia Pate followed in August 1841, wrecked at South Head with the loss of all 21 on board. The wrecks kept coming for over a century, the most recent being the yacht Aosky in 1994. Today, remains of lost vessels still surface under certain tidal and sand conditions, the harbour periodically revealing its collection of bones. A lighthouse was built on the Pouto Peninsula in 1884 to warn approaching ships, automated in 1947, closed in the mid-1950s, and renovated in 1982-84. The structure still stands, a monument to the hazard it could never fully eliminate.

European settlers began arriving in 1839 to fell and mill kauri trees, and the harbour became a timber highway. The Wairoa River feeds the Kaipara from the north, and thirty kilometres upstream, Dargaville was established as a mill town. The stretch of water between Dargaville and the harbour mouth is broad and straight, an easy route for navigation into what were then dense kauri forests. Ships of up to 3,000 tons carried timber and logs down the Wairoa, defied the treacherous bar at the harbour entrance, and continued on to other New Zealand ports or across the Tasman to Australia. Immigrants from Britain and Croatia were drawn to the area by the timber industry. From the south, Helensville established itself as a port on the Kaipara River from 1863. When the timber ran out, both towns reinvented themselves around sheep and dairy farming, and more recently vineyards and deer farms.

The Kaipara is a migratory bird habitat of international significance. Forty-two coastal species are known, and populations of up to 50,000 birds are common. Bar-tailed godwits fly from Alaska to feed here during the Southern Hemisphere summer before returning north to breed, a round trip of over 20,000 kilometres. Lesser knots and turnstones make similar journeys. Threatened native species crowd the harbour's mudflats and mangrove forests: North Island fernbirds, fairy terns, Australasian bitterns, banded rails, grey-faced petrels, and wrybills. The harbour includes 125 square kilometres of mangrove forest with subtidal fringes of seagrass, creating nursery habitat for both birds and fish. Black swans, pukeko, and grey ducks breed in the shallows. The Kaipara is the single most significant wetland for west coast fisheries and the largest estuarine harbour on the west coast of New Zealand.

The harbour is a drowned river valley system that first formed two to three million years ago as an open bay. Over time, elongated sand dune barriers grew across its mouth, creating the enclosed harbour. But the Kaipara has never been static. Over the last two million years, it has cycled between periods as a forested river valley and a flooded harbour, depending on global sea levels. The present harbour formed approximately 8,000 years ago, after the Last Glacial Maximum. Its 800-kilometre shoreline is the drainage catchment for about 640,000 hectares of land, fed by five rivers and over a hundred streams. The sand that makes the entrance so dangerous comes mainly from the Waikato River far to the south, carried northward by coastal currents. Some enters the harbour entrance, cycles back out, and continues its migration up the west coast. About 219,000 cubic metres of that sand is mined each year, contributing over half the sand requirements for Auckland's concrete and construction industry.