Natural Resources Wales (NRW) said it was taking water samples to find out the source of the pollution.
Officers are also taking the dead fish away for tests to find out what has killed them.
Other wildlife has not been affected and the water "seems clear", the environment body said.
Leon Williams, north Wales environment officer for NRW, added: "We will continue to keep an eye on the situation to make sure that there will not be any further incidents."
An investigation has begun after pollution killed more than 100 fish in the River Cefni on Anglesey.