We describe a magneto-gradiometric survey performed in the «Mar Piccolo» of Taranto, Italy in May 2005 for environmental purposes. This region, which is a noisy harbour environment, provides a challenging test for magnetic methods. To reduce spurious noise signals, with both temporal and spatial origins, we used two Geometrics G880 model caesium magnetometers towed in a transverse gradient configuration. We show how, in shallow waters, this gradiometric configuration allows us to distinguish anomalies due to small metallic bodies near the seabed from the induced noise due to the anthropic contribution and geomagnetic field variations. A direct visual inspection confirmed that the peculiarities highlighted in the gradient anomaly map were due to abandoned metallic objects found on the seabed.