The natural vegetation of Shakespear was largely destroyed when it was developed as a farm. When the land was purchased for a park in 1967 it was mostly cleared of almost all native vegetation except for parts of Waterfall Gully and Kowhai Glen, and patches of grazed manuka scrub in the campground gully. The freshwater wetlands at Shakespear would once have been extensive taking up all of the low lying land at Okoromai bay through to Army bay and Te Haruhi bay. The wetlands present today are much reduced and not always natural.

Puriri in Waterfall Gully

Waterfall Gully is one of the remaining areas of remnant forest, which consists primarily of taraire, tawaroa, karaka, pohutukawa, and puriri with small patches of kauri forest on the upper slopes of some of the ridges. The kowhai of Waterfall gully may be amongst the largest in the Auckland area, and the puriri particularly are very old and the taraire and kohekohe are prominent. The subcanopy is pigeonwood, mahoe, houpara/lancewood crosses, and cabbage trees. The understorey is karamu, Coprosma rhamnoides, hangehange, and mapou. Supplejack vines are abundant.

Kowhai Glen, the other area of remnant forest, has a canopy of pohutukawa, kowhai, taraire, and puriri. There are patches of naturally regenerating gumland scrub amongst the mature forest and the gully terminates in a wetland with a canopy of cabbage trees.

The original fresh water and saline wetland between Okoromai and Army Bays was drained when the park was first being developed as a Farm Park. A later change to Regional Parks policy has allowed a restoration plan for the Okoromai wetland. The LENZ map indicates patches of peatland in the Okoromai bay wetland which may once have had Baumea, Schoenus brevifolius , Empodisma minus (now a rare plant in Auckland) raupo, manuka and Dracophyllum lessonianum growing in it. There has been extensive planting of manuka, phormium (flax), and cabbage trees in the wetland area between Okoromai and Army Bays from 2007 until 2009.

The natural saltmarsh contains species such as glasswort (Sarcocornia) flats at Okoromai Bay and remnants of salt marsh ribbon wood and mangroves. There are more planted areas here than natural, and the natural sequences and environmental gradients are impacted by the drainage, raised causeways and haphazard placement of planted natives. There are plantings on the causeway (Heritage trail) of Chatham Island akeake (Olearia traversii), Norfolk Island hibiscus and some gums (Eucalyptus species).

An artificial pond at the base of Waterfall Gully has been colonised by native wetland plants and serves as a freshwater habitat for waterfowl. This is now densely packed with onion rush (Bolboschoenus fluvatilis). There is a cabbage tree/raupo swamp at the base of Kowhai Gully. It has been dominated by Mexican Devil (Ageratina adenophora) which is being gradually cleared by a number of volunteer groups.

Sea grass ( Zostera capricorni ) beds are present in both Okoromai Bay and Te Haruhi Bays.  Sea grass beds are considered to be an important marine ecosystem with high biodiversity and habitat values (e.g. for juvenile fish). They depend on good water clarity and are therefore sensitive to environmental changes (e.g. sedimentation). Sea grasses have been lost from some parts of Auckland e.g. the Waitemata Harbour and the Manukau Harbour . This reinforces the ARC approach of riparian planting to reduce siltation and maintain water clarity.

The dunes at Te Haruhi Bay and Okoromai Bay are in a sheltered harbour. Both bays have been extensively modified by kikuyu to provide a lawn for picnic/visitor arrival purposes. At Te Haruhi Bay the dunes are dominated by the exotic marram grass.

The dunes at Okoromai bay were probably always narrow and graded quickly into saltmarsh but this is difficult to tell considering the extensive modification.

The dunes are deepest near the campground in Te Haruhi Bay. Marram grass is dominant along most of the beach although there are some small patches of Pingao and a fair amount of Spinifex (most of which have been planted). Other dune species are the exotic grasses kikuyu and couch, harestail and the native Muehlenbeckia complexa and oioi (Ficinia nodosa). A dunes restoration plan includes continuing planting of Spinifex and Pingao as well as eradication of marram grass. It was recently noted when a major storm washed away recent plantings of spinifex that the small patches of Pingao were most resistant to destruction. Dune restoration also allows opportunities for threatened plant restoration e.g. Euphorbia glauca.