The sanctuary includes rock outcroppings and an intertidal marine ecosystem that is not found anywhere else in New York state.

[1][3] The island's flora largely consists of tracts of old-growth forest that existed prior to the settlement of the New York City area, as well as plants introduced by John Hunter in the 19th century.

[3] The Siwanoy Native Americans who originally occupied the area referred to the general vicinity around Hunter Island as "Laap-Ha-Wach King", or "place of stringing beads".

[1][10][24][15] One notable boulder, the "Gray Mare" at the northwestern shore of the island, is a glacial erratic where the Siwanoy would conduct ceremonies.

[28] By the early 1900s, Hunter Island had become a popular summer vacation destination, and it hosted a campsite.

[37][38] Hunter Island became popular with European immigrants who built shelters and established summer colonies.

[41][23][42] Moses devised plans for a new Orchard Beach recreation area after he saw the popularity of the Hunter Island campsite.

[35] At the time, the beach was a narrow sand bar connecting Hunter Island and Rodman's Neck.

[47] In the 1960s, there were plans to expand a landfill in Pelham Bay Park, which would have created the City's second-largest refuse disposal site next to Fresh Kills in Staten Island.

[5] A group of preservationists headed by Dr. Theodore Kazimiroff, a Bronx historian and head of the Bronx Historical Society, lobbied the city to create a wildlife preserve in Hunter Island, one of the sites where the landfill was proposed to be expanded.

[48][49] On October 11, 1967, Mayor John Lindsay signed a law authorizing in the creation of two wildlife refuges in Pelham Bay Park: the Thomas Pell Wildlife Sanctuary on the western side of the park, and the Hunter Island Marine Zoology and Geology Sanctuary on the former Hunter Island.

It was described as one of the finest mansions of the period, with three stories, a large veranda, and terraced gardens leading to the island's shore.

The main entrance faced west, toward the mainland, and contained a grand doorway flanked by columns.

[26] The mansion held an art collection of over 400 works from artists such as Rembrandt, Peter Paul Rubens, Anthony van Dyck, and Leonardo da Vinci.

[9][10] The entrance to the causeway from Eastern Boulevard (present-day Shore Road), on the mainland, was marked by two white granite gateposts.

The rocky coast of Twin Islands contains the southernmost outcropping of Hartland schist, the major bedrock component of New England coastlines, as well as granite with both migmatite dikes and veins made of quartz.

One can also find grape hyacinth, periwinkle, daylily, and Tartarian honeysuckle, which were part of the Hunter Mansion's garden.

[7] The Kazimiroff Nature Trail, as well as the Pelham Bay Park Environmental Center at Orchard Beach, opened in June 1986.

[7][54][56] Along the shared "lasso spur" is a canal for mosquito control as well as an intersection with the old Hunter Island causeway's cobblestone approach path.

[56] Going counterclockwise from the intersection with the two "loops", the trail passes through a grove of 100 Norway spruces planted in 1918; a black locust forest from the 1970s; and a thicket of shrubs and vines.

[57] At this point, the longer blue trail diverges to the northwest and then northeast, passing the former Hunter Mansion's knoll; a forest of white pines; some mugwort and invasive Ailanthus; the Hunter Mansion's main driveway; a less dense patch of trees and burnt tree stumps, part of a forest burned by the Siwanoy; white oaks and black locusts; and lichen-covered boulders, a rare occurrence in New York City parks.

[58] The shorter red trail goes directly north through a white poplar forest; a grove scorched by an uncontrolled fire; and remnants of the former estates' stone walls.

[59] Both trails merge and loop back to the east and south, passing through glacial-erratic boulders, New England bedrock, and the island's salt marsh.