[7] The peninsula was significantly modified by agricultural, residential and recreational developments until the 1980s causing overall ecosystem degradation, however protection, management and restoration efforts over the past 30 years has seen the area's biodiversity recover.

Today Phillip Island Nature Parks (PINP) manage the peninsula as an area of ecological significance under the Crown Land Reserves Act 1978.

[6] The peninsula is also home to two major state tourism assets managed by PINP, the Penguin Parade and the Nobbies Centre, which receive over 600,000 visitors annually.

[1][9] Vegetation communities are determined by wind exposure, salt-spray, soil composition, geology, presence of seabird colonies and past land management practices.

In 1839 the entire island (approximately 10,000 hectares) was cleared by burning to make way for agriculture, by 1872 farmers had settled the peninsula cultivating chicory and bringing cattle and rabbits which further decimated the land.

[13] Slowly the importance of protecting the area's natural values for the benefit of both wildlife and tourism were recognised and a large penguin reserve was established by the government.

[13][16] Research indicated that introduced predators, namely foxes, were adversely effecting breeding success and adult survival, and that habitat reduction and destruction due to developments was significantly depressing the population.

[13] Under this plan, the government instituted a buy-back program for all infrastructure on the Summerland Peninsula and allocated funds for substantial further scientific research into better understanding penguins on land and their lives at sea.

[8] The program included under-grounding power, demolition and removal of the last remaining houses and redundant infrastructure, revegetation and the provision of artificial nests and pest and predator control.

[6][7] Overall vegetation of the Summerland Peninsula is dominated by Coast Tussock-grass (Poa poiformis), Bower Spinach (Tetragonia implexicoma), Seaberry Saltbush (Rhagodia candolleana), Rounded Noon-flower (Disphyma crassifolium subsp.

African Boxthorn (Lycium ferocissimum), Gorse (Ulex europaeus), Kikuyu grass (Pennisetum clandestinum) and Melaleuca species have been given priority for management as they threaten seabird habitat and provide shelter for feral cats and foxes.

[6][7] Introduced species such as Marram Grass (Ammophila arenaria) and Sea Wheat-grass (Thinopyrum junceiforme) have become well-established in many areas affecting dune development and morphology.

[6] The peninsula also supports the Black Swamp Wallaby (Wallabia bicolor), Cape Barren Goose (Cereopsis novaehollandiae), Short-beaked Echidna (Tachyglossus aculeatus), Copperhead Snake (Austrelaps superbus), Blotched Blue-tongued Lizard (Tiliqua nigrolutea) and the threatened Growling Grass Frog (Litoria raniformis) found at Swan Lake.

[6][24] Surrounding waters are a feeding area for the Great White Shark (Carcharodon carcharias) listed as vulnerable in Australia under the EPBC Act.

[citation needed] Scientific research into little penguins has been ongoing in the area for 48 years, monitoring the colony both on land and at sea to better understand threats to population and breeding.

In 1995 a previously unknown Herpes virus infected millions of pilchards (Sardinops sagax) across Australia, at the same time increases in little penguin moralities were reported across western Victoria and numbers crossing the Summerland Beach declined.

[26][27] Approximately one million short-tailed shearwaters (commonly known as mutton birds in Australia) return to Phillip Island from the Bering Straits, Alaska to breed in burrows each year.

[10][32] Marine debris has been identified as a threat to the colony, with recent research estimating 302 entanglements occurring per year on Seal Rocks with pups and juveniles most at risk due to their inquisitive and playful nature.

[10][33] Current major threats to the biodiversity of the Summerland Peninsula include predation and competition from introduced species such as foxes, feral cats (Felis catus), rabbits (Oryctolagus cuniculus) and black rats (Rattus rattus) as well as loss and degradation of native plant and animal habitat from invasive pest plants, climate change, disease, impacts to food supply, fire, oil spills and general human disturbance.