Malta has been found guilty of not fulfilling its EU obligations under the Water Framework Directive and was ordered to pay the court fees.

However, the government insists the EU rules in question, which were drawn up before it joined, were not tailored to the island’s natural context and size.

The European Court of Justice said Malta failed to establish programmes to monitor lakes, reservoirs, streams, rivers, canals and coastal water, which it defines as “inland surface waters”. Malta also failed to submit summary reports on the monitoring programmes on the status of inland surface water.

The government said the Court did not challenge the “unique situation and scientific arguments” put forward by Malta, which said the scientific methods for monitoring surface waters could not be applied to the island.

The government argues the directive was negotiated and adopted in 2000, so Malta was not involved in the discussions and its “particular nature and size” was not taken into account in the law’s drafting.

“Malta’s inland surface waters are very small and generally temporary since water flow occurs mainly through rainfall. These features make them unique to the islands. Other technical considerations, such as lack of historical scientific data trends on Malta’s inland surface waters, make the scientific monitoring methods required by the directive unsuitable to Malta’s case,” the government argued.

It said Malta’s inland surface and transitional water bodies were aquatic and wetland habitats of high conservation value and were therefore already protected to a high degree under national legislation and under the EU Habitats Directive and the Birds Directive.

On the other hand, the ECJ said Malta’s pleas were inadmissible because they were presented in the wrong stage of proceedings.

It pointed out that, under its rules of procedure, no new plea could be introduced in the course of proceedings unless it was based on matters of law or facts which came to light in the course of the procedure.

A report submitted by Malta as the scientific basis of its reasoning was dated April 2008, over a year before the proceedings commenced.

“Therefore, the claims for dismissal of the substance of the action and the underlying pleas advanced for the first time in the rejoinder must be considered as late and, therefore, inadmissible,” the court said.

The government said it intended to liaise with the European Commission to identify “a practical way forward” to comply with the Court judgment in order to fulfil Malta’s obligations under the Water Framework Directive within the island’s scientific and geological realities.

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