People have reported dead fish in Aberaeron, Aberystwyth, Barmouth, Harlech and Chwilog.
Other beaches are also likely to be affected.
NRW experts said it was a "natural phenomenon" caused by mackerel and other fish chasing food in calm seas.
Rowland Sharp, marine fisheries officer for NRW, said: "The calm seas means that mackerel chase small fish all the way on to the beaches.
"The fish in these bait balls will ground themselves on beaches in an effort to escape."
He added: "It may appear worrying, but it's only nature at work really."
Reports of thousands of small fish being washed up on beaches in Ceredigion and Gwynedd are no cause for concern, said Natural Resources Wales (NRW).