A dead black-winged stilt was found at the Għadira nature reserve after it was shot on Thursday morning, BirdLife Malta claimed.
The bird, which is protected under the EU Birds Directive, had gunshot injuries that included a broken leg and bill.
The adult male bird visited the reserve over the past weeks and paired up with an adult female, showing courtship behaviour.
The female also had gunshot damage to her left wing and was seen calling for the male, according to the NGO.