St. Croix Island is not large. It runs 700 meters along a northwest-southeast axis and is about 360 meters wide at its broadest point along the west coast. The highest point sits halfway along the north coast, 58 meters above sea level according to BirdLife International. The island is rocky, with minimal vegetation, and two disused stone bungalows built first for guano collectors and later used by the University of Port Elizabeth for research purposes are among the only structures. What the island lacks in size it compensates in ecological weight. With approximately 22,000 African penguins breeding here, St. Croix supports the single largest colony of a species whose total population has plummeted by more than 95 percent since the early 1900s. The colony peaked at 63,000 birds in 1993. The decline since then mirrors the species-wide crisis, driven by competition with commercial fishing for sardines and anchovies, oil pollution, and habitat disturbance.

St. Croix is the principal island in a group of three that includes Brenton Island, named after Naval Commissioner Sir Jahleel Brenton, and Jahleel Island, also named in his honor. Brenton sits 1.75 kilometers south, a low islet of less than 20 meters elevation, 5.75 kilometers from the mainland. Jahleel is the most accessible, just over a kilometer from the closest beach and within sight of the Port of Ngqura's 2.6-kilometer eastern breakwater. All three islands and their surrounding waters are declared nature reserves within the Addo Elephant National Park and are closed to public access. The islands hold a locally significant breeding population of Cape cormorants alongside the penguins, and boat trips from Gqeberha (Port Elizabeth) bring visitors close enough to observe the colonies without landing. From these boats, the penguins are visible as dense clusters of black and white on the island's gray rock, their braying calls audible over the engine noise.

The proximity of St. Croix to the Port of Ngqura creates a tension that conservation groups have been sounding alarms about for years. The deep-water port facility at Coega, on the northeastern outskirts of Gqeberha, lies within eight kilometers of the island. In 2019, an oil spill at the port directly impacted the penguin colony, coating birds in fuel that destroys the waterproofing of their feathers and exposes them to hypothermia. The conservation group SANCCOB has led efforts to clean and rehabilitate oiled penguins, but the work is painstaking and the threats keep growing. As of 2022, no environmental impact assessment had been conducted on ship-to-shore fuel bunkering operations in the bay, despite further spills threatening the breeding colonies. The African penguin is classified as endangered, and scientists estimate that at current rates of decline the species could be functionally extinct in the wild within decades. St. Croix is one of the few colonies still large enough to sustain itself, but that margin narrows with each spill, each fishing trawler, each year of warming seas.