The fish are thought to have perished due to a lack of oxygen in the water - depleted by the duckweed which multiplies in hot, dry weather. The presence of an invasive weed called Azolla is also exacerbating the problem.
But now concerns have been raised that the carpet of green vegetation could prove a danger to people and pets too.
As reported earlier this month, the thick vegetation has been causing problems to those using the waterway – with sports and recreational activities having to be cancelled.
The Canal and River Trust (CRT) previously said they have been sending out weed boats several times a week in an attempt to clear some of it.
However, it hasn’t been enough to help the aquatic wildlife there – with a high number of dead fish now floating in the waterway.
Commenting via Twitter, one reader wrote: “There are dead fish everywhere – awful!” Another tweeted: “When I walked down the river at the country park at 6am the river looked like a grass path.”
Bod Meeds, commenting via Facebook, said: “There must be hundreds of thousands dead here. The stench of all these rotting fish is unbearable.”
Bod raised concerns about how the thick river weed could now be a danger to people and pets.
He is certainly not alone in his concerns, with several readers contacting us to voice their fears.
Annie Edkins emailed us after her cat fell into the river after walking onto the weed thinking it was grass.
"The green carpet of weeds covering the surface is now so thick you can see it in inches and no water is visible,” she said. “The birds now walk across the surface.
"The two things that concern me - the wildlife in the water must be in distress, but the bigger issue is the tragedy just waiting to happen.
"We have already had a pet, who thought it was grass, go into the water. Thankfully he got out safely.
"The thicker the surface gets though the more likely animals might think it's a solid surface. Add to that if a person, heaven forbid a child, decided to try to rescue the animal, or a child thought it could reach a lost ball, then the result could easily be fatal.”
A spokesperson for the Environment Agency said: “The Environment Agency are working with the Canal and Rivers Trust to respond to fish in distress on the River Witham in Boston.
“Officers have opened sluice gates to flush the build-up of surface vegetation and improve the water quality. The situation is improving but we continue to monitor the situation closely and are ready to respond.
“We will continue to review the situation and support the Canal and Rivers Trust as they continue their vegetation management work. The warm weather and extremely low rainfall in the last few months has led to high levels of weed growth and low flows. If you see fish in distress please report it to 0800 807060.”