Hopefully we'll get some more details on what's hinted at in this Times of Malta piece:

The Archaeological Society of Malta has called for the appropriate legal steps to be taken against those responsible for any possible disturbance and destruction of the Roman port remains exposed during trench works in Marsa.

The society said a public inquiry should be ordered since in the opinion of qualified archaeologists, trenching and digging works in the vicinity of the Old Tram Station in Marsa were damaging the archaeological remains.

The issue was broached in yesterday's issue of The Times, which reported that the Superintendent of Cultural Heritage Anthony Pace had asked for the designs for a new storm water channel to be revised if further damage is to be stopped.

The society recommended that professional archaeologists carry out a thorough investigation of the exposed features and possibly of those that may lie buried in the area.

"Such deposits are simply irreplaceable and their loss would mean the loss of significant information concerning Malta's Roman and possibly Byzantine past," society president Patricia Camilleri said. [...]

An article from Friday, which I missed somehow, gives some more hints:

[...]

Considerable archaeological remains extend over most of the footprint of the proposed storm water channel project near Jetties Wharf, Marsa.

Officials from the Superintendence of Cultural Heritage have for the past three weeks been monitoring earth clearance at the site in question after the workers accidentally unearthed the Roman remains.

[...]

The discovery of ancient harbours is not a usual occurrence and such sites are of inestimable importance for the maritime history of the Mediterranean. The remains spotted today are likely to be the same as those documented in the Museums Department's annual reports of the 1940s and 1950s.

Timmy Gambin, a specialist in ports from the ancient period to the Middle Ages, has described Marsa as an extremely important Roman port in days gone by.

A large Roman town existed in the environs of Marsa, a town that housed people associated with maritime related services including merchants, shipwrights, stevedores and rope makers.

Discoveries add fuel to this theory. In the 1760s, a huge Roman warehouse complex was discovered in Jesuits Hill under the power station. In the 1950s another complex was found near Racecourse Street while in 1956 yet another large complex came to light under the Marsa school where the current excavations are taking place.

The Romans built these harbours as part of a network of havens for the transport of grain, Mr Gambin had said.

The remains strongly suggest that the port at Marsa not only served local needs but also those of Roman ships and traders operating throughout the Mediterranean when Malta was very much part of the connectivity in the Roman world.

I wonder if there are remains of shipwrecks nearby ...