Conservationists in the southern African country spent months investigating after elephant carcasses were first spotted along the Okvango Delta at the start of May.
On Monday, a national park spokesperson told a news conference that 330 animals had been killed after drinking contaminated water.
Cyril Taolo, deputy director of the Department of Wildlife and National Parks, said this had been caused by a "toxic bloom" of algae.
The unexplained deaths ceased after the watering holes dried up, Mr Taolo confirmed.
Both male and female elephants of all ages died, with clinical signs limited to neurologic symptoms, he explained.
The deaths happened mainly near seasonal water basins and did not spread beyond the initially affected region.
However, Mr Taolo added, no other wildlife species were affected by the blue-green bacteria.
Even scavengers, like hyenas and vultures, observed feeding on the elephant carcasses showed no signs of illness, he said.
It remains unclear why the toxins did not harm other animals. Mr Taola also ruled out human efforts like anthrax, poaching and sabotage.
The department's principal veterinary officer Mmadi Reuben told the same conference that many questions remained unanswered.
Read More
"Our latest tests have detected cyanobacterial neurotoxins to be the cause of deaths. These are bacteria found in water," Dr Reuben said.
"However we have many questions still to be answered such as why the elephants only (died) and why that area only.
"We have a number of hypotheses we are investigating."
Botswana, is home to an estimated 130,000 elephants – almost a third of the continent's total.
In neighbouring Zimbabwe more than 20 elephant carcasses were discovered near the country's biggest game park.
Authorities suspect they succumbed to a bacterial infection.