CANBERRA, AAP – Drought continues to bite across parts of Queensland and NSW despite significant rain breaking the dry spell in the southern Murray-Darling Basin.

Latest figures show water storages across the entire river system sit at 54 per cent.

Dams in the northern basin are at 27 per cent, showing the rainfall gap for farmers and other water users to the south.

All parts of Queensland in the basin remain officially in drought while northern and far-western NSW are awaiting significant rainfall to replenish river systems.

Murray-Darling Basin Authority river management boss Andrew Reynolds says the results demonstrate how patchy rainfall has been.

“The northern basin’s water storage levels have started the year lower than we’d hoped, despite the influence of La Nina,” he said on Thursday.

“Persistent above-average rainfall is needed to turn around this long-term drought.”

Areas that received healthy flows early last year are once again struggling.

In the Barwon-Darling, the NSW government has enacted a new rule preventing water coming through being taken by some irrigators until there are improved flows.

“Protecting water in this way for downstream communities and ecosystems strikes a balance with upstream needs to also access water,” Mr Reynolds said.

The Commonwealth Environmental Water Holder is delivering water into the upper Barwon River system from the Gwydir and Macintyre rivers.

Mr Reynolds said in contrast with the north, most of the southern Basin benefited from reasonable rain in the past few months.

State water allocations are up to 100 per cent for some Victorian licences and in regions such as the Murrumbidgee.

“Water quality issues continue to be a watchpoint for the MDBA and state agencies, due to the ongoing risk of hypoxic blackwater,” Mr Reynolds said.

“We also encourage people to be alert to blue-green algae outbreaks, which have been occurring in several parts of the River Murray and in storages in Victoria and the northern Basin.”