If you are visiting Clapham Junction the caves are quite easy to find. Just walk a few couple of dozen yards uphill to the top of the limestone area and you're there.
Back in geological time the caves were all underground but then as tends to happen with limestone, the roof of the largest cave or a series of caves collapsed leaving a large cavity in the ground with a number of caves many of which are interlinked, around the margins. It's well worth scrambling down into the caves, they are lovely and cool and provide a bit of welcome shade from the Maltese sun.
The caves were occupied up until the nineteenth century and when you climb down into them you can see evidence of walls and entrances. Solid evidence of prehistoric occupation has yet to be found in the caves but considering that a set of cart ruts start on the margins of the caves I'm sure this site would not have gone unnoticed by the prehistoric Maltese.