The outlook for the environment in the Murray-Darling Basin, particularly in the north, is extremely challenging and there will be almost no scope for environmental flows for the remainder of the 2018-19 year unless it rains, the Murray-Darling Basin Authority has warned.

It says the focus will be “on providing drought refuges and avoiding irreversible loss of species”.

Releasing its environmental watering outlook for 2019-20 the authority warns that there are almost no reserves of environmental water in the northern basin and that, as a result of above-average temperatures and low inflows over successive years, some important wetlands and floodplain forests have not received water for long periods.

It says conditions in the Coorong, a Ramsar-listed wetland in South Australia, are deteriorating, as are conditions in the Narran Lakes, despite the federal government paying $80m for water rights aimed at restoring them. The Macquarie Marshes and floodplains along the Murray are also deteriorating.

The report says the conditions in the lower Darling are particularly severe and the length and duration of cease-to-flow events in the lower Darling has skyrocketed since 2000. It acknowledges this is due to extraction by irrigators upstream as well as climate.

“The hydrology in this area has changed in recent years ... an effect which can be tied to both the volume of water extracted from the river and climate across the northern basin,” it says.

“This trend has also affected water availability in Menindee Lakes and the flow characteristics downstream through the lower Darling,” it says.

“For flows measured at Weir 32 on the lower Darling [at Menindee] for the period of 1982 through to 2000 there were no cease-to-flow days (flow below 5ML/d). In the following 18 years, from 2000 to 2018, there were 499 cease-to-flow days; 219 of these fell in the last few years, including the cease-to-flow period starting in late 2018.”

The MDBA pats itself on the back for successfully engineering one environmental flow in 2018, saying state and commonwealth agencies worked together to deliver water for the environment in the northern basin from April to June 2018” and provided 23GL for environmental flows.

But these operations are unlikely to be repeated in 2019-20 unless there is significant rain.

The report found there was a reduced number of waterbird species in the northern basin wetlands and “little to no waterbird breeding”.

A 2017 survey found the condition of native fish “remained poor” and since then there have been major fish kills. The MDBA does not speculate on whether there will be more fish deaths, but warns that environmental flows, if they occur, will need to be managed carefully to avoid exacerbating the situation by pushing polluted or de-oxygenated water downstream.

“It will take many years of good conditions for the [fish] populations in the lower Darling to recover,” the MDBA report says.

The situation in the Murray is a little better but the MDBA says there are challenges mainly in providing water to floodplains in the future. At the end of January the Dartmouth reservoir had 67% and the Hume 33% of its capacity.

The MDBA will be consulting on the priorities before releasing a final report in June.

Meanwhile the Academy of Sciences is expected to release its report on the causes of the fish kills, which was commissioned by the opposition leader, Bill Shorten, early next week.

It is expected to highlight the huge increase in cease-to-flow days at Menindee.