Two swans were shot and left in water near Aberdare.
The incident is believed to have taken place earlier this week after concerns were raised by members of the public.
RSPCA Cymru described the incident as "very worrying".
A spokesman said: " The RSPCA has received very worrying reports alleging two cygnets have been shot in the Aberdare area, at water near a superstore on Cae Alaw Goch.
"If anyone has more information on this alleged incident, we'd urge them to contact our emergency line on 0300 1234 999."
South Wales Police also confirmed officers have been notified of the incident.
A statement provided by the force read: "On July 21, 2020, two deceased cygnets were sighted by a member of the public in a body of water between Aberdare and Cwmbach.
"At this stage it is unknown how the birds perished but we are working with the RSPB, and once this is established we will be in a position to consider the most appropriate course of action.
"Any element of foul play or cruelty will be investigated."
If you have any information about the incident you are urged to call 101, and provide reference number 259772 while making a report.
