The metaphor is one of hope, which is all that the Patriagiani movement has at this stage of the war. Nevertheless, the waters are shallow, meaning that the foundations of Mussolini's Fascist regime are shaky, to say the least. Roberto, like the other partisans, is convinced that if the resistance movement can grow in number and build support among the Italian people, it will be laying down more secure foundations for the future.

Individually, stones may be nothing, but in combination they can build a strong, impenetrable wall. By himself, Roberto is incapable of challenging the Fascists and their German allies. Though passionately committed to the partisan cause and keen to fight, he cannot do anything on his own. He needs other "stones" alongside him to make the fight worthwhile, just as he will need to combine with them to help rebuild Italy once Mussolini has been defeated and the war is over.

The Partriagiani Movement was a resistance force in Italyduring WWII, fighting underground against Mussolini, the fascists, and the Axis powers. The phrase recalls several events, which accrue into the final metaphor.  “Water” signifies Venice, the home of the two boys, and it also reminds us of Enzo bathing in the river, which causes him to be discovered a Jew when someone sees he is circumcised. As enotes points out (see link below), “Stones will always speak to Roberto of [Napoli], a friend who wove him tales old and new, and the stones to build himself anew.” More broadly, “stones”  refer to both Roberto and Enzo as  well as everyone else who joins the partigiani movement to rebuild the country after the war. Altogether, the metaphor suggests the determination and spirit necessary to rebuild their country after the devastation of the war. With enough people with the strength and spirit such as that of Roberto, anything is possible.