Dead dolphins and rotting fish could become a frequent feature on South Australian beaches due to warming seas.

Record high sea surface temperatures from summer to April caused thousands of small fish to wash up dead in SA gulf waters.

It stressed 33 dolphins to the point they succumbed to a virus normally suppressed by immunity.

Biosecurity SA aquatic pests manager, Vic Neverauskas, said it was logical to assume a higher risk of similar events because seas were following a warming trend due to climate change.

Fish that littered beaches on both sides of the Spencer Gulf and Gulf of St Vincent from 6 March to 26 April were linked to warm waters prolonging the life of naturally occurring algae caused by a three-day “upwelling” event – when winds work against the earth’s rotation to suck nutrient-rich waters from beyond the continental shelf and into shallow waters.

“As the month of March progressed, we kept getting increased algal blooms and increased quantities of algae, which we’ve been able to document with Nasa satellite imagery,” Neverauskas said.

Small territorial fish litter Spencer Gulf beaches near Port Neil, Eyre peninsula, the site of the first deaths on 6 March. Photograph: /Department of Primary Industries and Resources of South Australia Photograph: Department of Primary Industries and Resources of South Australia

South-easterly winds started events by trapping waters up to 5C above average against the west shoreline of both gulfs, killing scores of small territorial fish with heat stress.

Winds shifted westerly on 20 March, pushing warm waters to the east, and leading to the emergence off Adelaide’s metropolitan coast of a Chaetoceros diatom – algae equipped with barbs that latch onto fish gills and cause inflammation until the fish choke on their own phlegm.

“Ninety-nine per cent of the fish affected were small-bodied reef dwellers such as the pygmy leatherjacket,” Neverauskas said.

“But following Good Friday’s mortality event we also had small numbers of bream, a few morwong, a handful of whiting species and an unconfirmed report of a snapper.”

Flinders University oceanography lecturer and researcher Jochen Kaempf was not satisfied with the “official” explanation and wanted answers about the Port Stanvac desalination plant.

Environmental Protection Agency (EPA) data from nearby monitoring showed that ambient salinity dropped sharply on 22 March.

A possible explanation is a discharge event that added nutrients to the water and encouraged algae growth.

A spokesperson for SA Water said the quality of water discharged to the ocean from the desalination plant had not changed since October 2011 when it first started producing water.

An EPA spokesperson said there were no out of the ordinary discharges at the time and the plant had been operating without any “exceedences of licence conditions”.

Indo-Pacific bottlenose dolphins also washed up dead throughout the Gulf of St Vincent and surrounding waters from 1 March until 7 May.

University of Adelaide veterinary diagnostic laboratory operational manager Dr Stephen Pyecroft said the dolphins were likely to have been killed by the morbillivirus, a virus transmitted by close contact between dolphins.

Affected dolphins were mostly juvenile and likely to have been immuno-suppressed for a variety of reasons, including heat stress, although pathological results remained pending.

“I just think that the water temperatures and the oceanographic conditions that have been shown in the last three to four months is pretty telling,” Pyecroft said.

“And if the prediction is that changing climate patterns are going to leave warm waters and algae blooms sitting there for months, then it’s going to affect the natural aquatic environment that these animals live in.”

Kaempf said the mortality events required a more rigorous scientific approach to include all possibilities, including pollution.

“Some scientists say climate change is going to bring more extreme weather events, and that means algal blooms are going to happen more and more often.

“This is about finding the nutrient sources that cause algae blooms in warm water.”

According to the EPA, Adelaide coastal waters’ nutrient load decreased from 2,891 tonnes of nitrogen a year in 2003 to 1,594 tonnes a year in 2008, while sediment loads decreased from 10,999 tonnes a year to 7,525 tonnes a year.

Nitrogen discharges from wastewater treatment plants and industry increased by 35 tonnes in 2012, probably as a result of slight reductions in reuse due to higher rainfall.

“With the aimed reduction in nutrient loads entering the marine environment over the next few decades, it is hoped this will reduce the likelihood of major algal blooms due to nutrient enrichment and temperature increases,” the EPA spokesperson said.

“However, upwelling events are unpredictable and their role in algal blooms in the gulf is not well understood.”

Acting SA food and fisheries minister, Grace Portolesi, said the algal bloom was an isolated event caused by the “rare warming” of coastal waters and could not yet be attributed to climate change.

“While these types of events are rare and unfortunate, understanding their cause and how best to respond to them is something that requires further research and investigation,” she said.