The Scottish Environment Protection Agency was called in after thousand of sprats had apparently been killed by pollution.
Dozens of the tiny fish were seen floating on the surface in the dockyard at the former naval base in Rosyth, Fife.
But it was found that the sprats had been trapped in the tidal basin when the gates had been opened to allow a ship in, and they have little or no hope of surviving.
A spokeswoman for SEPA said, “We will not be taking any more action, as we have established there is no pollution.
“Unfortunately, if the gates are reopened, then more fish will just swim in. “This type of fish needs plenty of oxygen and tidal waters to survive.
“And the fish that are there will be using up the supplies of oxygen already in the water.”
A spokesman for Babcock Rosyth Defence said: “We have made some attempts to drive the fish out with boats but it is only possible at low tides because we don’t want to let any more in.
“We have also been using an air hose to try to get some more oxygen into the water.”
