Fish stocks have been decimated on the River Thurne, after Norfolk was hit by floods.
High tides and gales on Tuesday night caused seawater to surge upriver, killing fish in their thousands.
Worst-hit was the Thurne at Potter Heigham, where the Environment Agency said it had received countless reports of dead fish of all species.
An EA spokesman said: "Tens of thousands of fish have been found dead at Potter Heigham in the biggest incident like this we have had for 15 years.
"Because of the storms, salt water washed in and freshwater fish can't cope with that."
While salt tides have practically wiped out the Thurne system's pike periodically over the last century or so, their prey appeared to have borne the brunt of casualties, with large numbers of roach, bream and rudd dead.
When salt tides are expected, the agency usually puts down a barrier at Herbert Woods boatyard, in Potter Heigham, which allows fish to find sanctuary in freshwater.
But experts think the recent mild weather has meant fish have been shoaled further downstream than normal and so were unable to escape the tide.
Thousands of fish were also killed when the River Chet burst its banks near Loddon.
But today the EA said salt levels were falling and rain was expected to help flows push salt downstream.
Wednesday morning saw parts of the Yare and Waveney valleys flooded by what were described as the highest tides for 40 years. Cars and riverside properties were under feet of water at Brundall, near Norwich.
A sea angler was feared drowned after he was washed away by a freak wave at Kessingland Beach, near Lowestoft, on Wednesday morning. He was later named as 41-year-old Martyn Franklin, from Lowestoft.
More here .
