Low rainfall, blockages and diverted flows are blamed for sections of the river drying out on the border between Essex and Suffolk.
The Environment Agency hopes heavy rain this weekend will provide enough water to partly re-fill the River Stour.
Debris blocking flows at the Bures Mill is preventing boats navigating downstream.
Water from boreholes pumped in to river channels between Bures and Nayland could improve levels, the agency said.
It added that water had been diverted to reservoirs over the past few weeks, but the drop in levels at Bures Mill has been caused by debris under the water gate which has blocked flows.
The river rises in east Cambridgeshire and forms most of the border between Essex and Suffolk, flowing east of Haverhill through Sudbury before opening out into an estuary at Manningtree and heading onwards to Harwich Harbour and the North Sea.
Parts of the river have been immortalised in the paintings of John Constable.
“We’re hopeful a combination of the boreholes we have switched on upstream, pumping additional water into the river, and the forecast rain, will increase flows and push out the blockage,” an Environment Agency spokesman said.
“If not our staff will need to intervene and this will involve draining part of the river which will cause disruption for recreational users through Bures.
“We will continue to monitor the situation and will be sending teams out regularly this week to check the areas where fish may become trapped.
“At present there are no signs of any dead fish or fish in distress.”
A section of the Stour in Nayland has temporarily run dry, although water is flowing through the Mill Stream, which provides an alternative channel for the river.
“We are seeing low flows in a number of Suffolk and Essex rivers due to the dry weather,” the spokesman said.
Water from the boreholes is expected to reach the affected parts of the river within the next few days.