Before colonisation, the Port River region and the estuary area were known as Yerta Bulti (or Yertabulti) by the Kaurna people, and used extensively as a source of food and plant materials to fashion artefacts used in daily life.

The rich ecosystem of the river, which includes mangroves, seagrass, waterbirds, and abundant marine life, has been historically impacted by industrialisation and associated pollution.

"[3][4] Prior to the 1836 British colonisation of South Australia, the river was a shallow and narrow tidal creek winding between mangrove swamps.

[6][7] The Kaurna people made use of the natural resources; for example, they used to trap and spear fish (kuya), lobsters (ngaultaltya) and birds (parriparu), and also gathered bird's eggs, black river mussels (kakirra, species Alathyria jacksoni[8]), periwinkle (kulutunumi), river crawfish (kunggurla – probably common yabby[9]), clams, native mud oysters and blue swimmer crabs.

[1] At that time, a large sand dune known as the Gillman Dunal system stretched inland across the southern part of the area, where the people camped for years even after European settlement.

[5] The initial landing place in Adelaide, chosen by Colonel William Light in late November 1836, was south of the current port and is now part of West Lakes.

[2] In 1837 a harbour was declared when harbourmaster Captain Thomas Lipson took up residence on the shore of the then named port creek with the first migrants landing in the same year,[12] onto the river bank lined with mangroves, until a canal was cut through them to a higher location in the sand dunes.

[11] This new harbour allowed the larger steamships that were then arriving at Adelaide to dock, with smaller steam vessels and sailboats able to use the old port facilities.

The Torrens used to flow north-west into the Port River, until sediment accumulated upstream built up, blocking the channels and forming a large area of marshland known as "the Reedbeds" across some of the present western suburbs.

[citation needed] Section Banks is artificial island made of seashell-grit, clay and sand, around 1,600 metres (5,200 ft) long, created partly by natural processes but also by manmade construction, at the northern end of the Outer Harbor breakwater.

The worst environmental disaster to occur in South Australian marine waters was the St Kilda salt fields brine spill, which killed of hectares of mangroves, samphires and other vegetation.

After water pollution levels were shown to have improved in December 2016, the annual "Long Swim" recommenced in the Inner Harbour, after a hiatus of some years.

[1] The Port Adelaide Kaurna Cultural Heritage Trail is marked nearby to the Ship's Graveyard,[27] and extends to both sides of the river between the two bridges.

Several wrecks lie in a "ship graveyard" between the Outer Harbor railway line bridge and the Jervois Bridge:[32] the ketch Alert, barge Trafalgar, schooner Fides, the timber hulk Fitzjames (which was for some time a floating boys' reformatory, later relocated to Magill Reformatory),[27] the Fish Market Pontoon, and the Unnamed Pontoon.

[11] The ecology of the estuarine area includes and is dependent on the health of its component parts: the waters, intertidal zone, and lands on the shore.

[15][16][17] In their natural state, the interconnected creeks and channels of the Port River estuary and Barker Inlet were surrounded by mudflats, mangroves, and saltmarshes colonised by samphires.

Flows occur from the north (via Outer Harbor) and south (West Lakes, which draws in seawater via an engineered tunnel at Grange).

[38] Since construction of the Breakout Creek outlet in 1937 to drain the Reedbeds (see above),[15][16][17] and the closure of the former Port Adelaide Wastewater Treatment Plant with the diversion of wastewater to Bolivar Waste Water Treatment Plant in 2005, the upper reaches of the Port River now receive only limited amounts of locally derived stormwater, and are now largely marine.

Flushing of West Lakes occurs through a one-way system that draws in seawater from the Gulf through an inlet off the coast at the southern end.

In December 2016, SA Health testing showed very low counts of bacteria, enabling the annual "Long Swim" in the Inner Harbour to recommence after many decades of absence.

[1] Mangrove forests (consisting of only one species, Avicennia marina var resinifera) remain at Ethelton and New Port, along the shores of Torrens Island, the North Arm (which connects to Barker Inlet) and adjacent to the Mutton Cove Conservation Reserve on the Lefevre Peninsula.

[40] Attempts are being made to restore the once extensive reefs of shellfish, including native mud oysters (ostrea angasi), cockles, and razorfish (pinna bicolor[41][42]), which had almost disappeared since European settlement.

This ban, combined with growing populations of native oysters and razorfish, has led to benefits, such as improving the water quality due to their filter feeding, and providing habitat favoured by other species, such as whiting, bream, and blue swimmer crabs.

[13] The Hercules club mud whelk (Pyrazus ebeninus), which is most abundant in tropical or subtropical waters off Queensland and New South Wales, had not been detected in the Port River since the last ice age around 10,000 years ago.

Scientists surmise that they were seeded there by ballast water brought in by ships, and the razorfish and oyster beds provide a nursery for breeding.

[47][48] Climate change is resulting in rising sea levels that threaten to cause erosion and further loss of the mudflats, salt-marsh and mangroves, exacerbated by land subsidence.