Two ducks were killed at the Marsascala saline marshland known as Il-Magħluq tal-Baħar, which was vandalised.
Nature Trust Malta reported that a number of dead ducks were also spotted floating in the water there, but the cause of death was unknown.
The sensitive ecology of the area was being increasingly damaged by duck droppings, vandalism and littering, the NGO said.
The ducks, which Nature Trust noted were not a natural part of the habitat, were a cause for concern from an ecological point of view. They attracted rats which, disturbed by the construction of the new bypass, had infested the roads and the marshland until the local council took action.
“While we urge the authorities to relocate the ducks, we do not tolerate animal cruelty, even if the ducks are problematic,” Nature Trust executive president Vince Attard told Times of Malta.
Il-Magħluq is a Natura 2000 site (part of an EU-wide network of protected areas), classified as a special area of conservation (SAC). It is mainly a body of brackish water that was originally two fish ponds lined with layered stones.
A saline marshland also exists around the periphery of the pools, which represents one of a few existing marshlands in the Maltese Islands and one of only two in the south.
The most important species in this site is arguably the endemic Maltese killifish (il-bużaqq).
Adi Associates, an environment and planning consultancy firm, together with Greek company Epsilon International SA, were contracted by the Malta Environment and Planning Authority to draw up management plans for all terrestrial Natura 2000 sites.
The consultancy firm has already received feedback from interested individuals, according to Adi Associates managing director Adrian Mallia. “The site, though important, has unfortunately been subjected to abuse from vandalism and, especially, chronic littering,” he said.
“But possibly the biggest problem it faces is the fact that the original link with the sea was negatively affected during the redesign and reconstruction of the road running between the ponds and the sea.”
Although pipes were laid beneath the road, the job was not done properly and they were not large enough or adequately maintained to cater for the flow required by this habitat, Mr Mallia said. This would need to be rectified for the site to function properly, he added.
An additional problem is the input of fertiliser from the adjacent agricultural land that is causing the death of organisms such as fish.
“The presence of the ducks is itself contributing to additional problems from their excrements.
“If one had to properly manage their numbers, a small amount would not necessarily impact the ecological integrity of the Natura 2000 site. What is certain is that, if they are to be removed, any intervention should be done humanely and without suffering for the animals,” Mr Mallia said.
Other sources pollute the ponds, in particular surface water run-off from the adjacent roads (complete with all road debris and oils) that is discharged directly into the ponds, affecting the quality of the water and introducing unwanted sediments and chemicals.
“The management plan for Il-Magħluq will seek to address these and other issues but will also attempt to engage the community at Marsascala and other interested parties to turn the site into a meaningful one for the locality instead of the nuisance it may currently be,” Mr Mallia said.