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."

Ten incidents of possible police misconduct have been found by investigators looking into the killing of Jacqueline Oakes.
Marcus Musgrove was jailed in July 2014 for killing the 51-year-old.
A review was launched over her death, including contact she had with various agencies at the time.
The Independent Police Complaints Commission said it had issued notices to 26 serving West Midlands Police officers and seven police staff, advising them they are subject to investigation.
Notices have also been sent to an officer who has retired and to one who now works at another force.
An IPCC spokesman said its initial assessment had identified ten potential misconduct issues relating to incidents between April 2013 and January 2014.
"Our independent investigation is looking at whether the police officers and staff involved resourced, recorded and risk assessed the incidents in line with force domestic abuse policy," the spokesman said.
A domestic homicide review is also being carried out by Birmingham Community Safety Partnership.
Ms Oakes was discovered in a bedroom at Century Tower, Dollery Drive in Edgbaston, in January 2014.
The mother-of-four died from multiple blunt force injuries.
Musgrove, of Lichfield Road, Aston, aged 40 when sentenced, was told he would serve a minimum of 18 years.
At the time, West Midlands Police said he carried out the fatal attack after weeks of subjecting her to controlling and abusive behaviour.

The Society of Motor Manufacturers and Traders (SMMT) said sales were up 8.4% compared with February last year.
Sales of alternatively fuelled vehicles jumped 19.9% year-on-year, with diesels up 5.6%.
Fleet sales fell 1.4% but still accounted for 53.1% of new vehicle sales in the month.
SMMT chief executive Mike Hawes said: "February is typically one of the quietest months of the year ahead of March's plate change, but this positive performance is encouraging and puts the sector in a good position for the coming 12 months."
Samuel Tombs, chief UK economist at Pantheon Macroeconomics, said only 4% of cars typically were registered in February, so "small movements in the absolute number of registrations have a big impact on the headline growth number".
"High consumer confidence, lower petrol prices and cheaper unsecured credit have enhanced the attractiveness of car ownership, but these drivers will be less supportive of sales growth in 2016," he added.
"Growth in car sales therefore looks likely to moderate, contributing to a slowdown in the overall consumer spending recovery this year."
A record 2.63 million new vehicles were registered last year - about 6% higher than in 2014 and the fourth consecutive year of growth, according to the SMMT.
The top selling models in February were the Ford Fiesta, Volkswagen Golf and Nissan Qashqai.
VW sales were down 13% compared with February 2015, although Toyota recorded a 16% drop and Vauxhall a 17% slide.
Ford sales were 12% higher compared with February 2015 at 11,513 vehicles,
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).
[NEXT_CONCEPT]
Thirty-five members and former members of West Midlands Police are being investigated over events that led to a woman's murder in Birmingham.
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Almost 84,000 new cars were sold in February in the UK - the highest level for the month since 2004.