The first we hear of one of Antonio's ships having been wrecked is in Act 3, scene 1 when Salarino reports the rumour going around the Rialto to Salanio upon his enquiry. He tells Salanio in part:
Why, yet it lives there uncheck'd that Antonio hath
a ship of rich lading wrecked on the narrow seas;
the Goodwins, I think they call the place;...
It is clear that Shylock had also heard the rumour for he calls Antonio 'bankrupt,' 'prodigal' and a 'beggar.' He furthermore states that Antonio should look to his bond because it is time for the loan to be repaid and he, Shylock, will claim forfeit and demand a pound of the merchant's flesh.
Tubal later confirms that Antonio had indeed lost a ship. Tubal tells Shylock that he had spoken to some of the sailors who had escaped the wreck. The Jew is happy at the news and sees it as beneficial to him for he can then exact his revenge.
We again read of Antonio's misfortune when Bassanio, who is at Belmont, receives an urgent letter from Antonio informing him about the situation. This time, however, it appears as if Antonio has lost more than just one ship, for Bassanio asks Salarino, the messenger:
But is it true, Salerio?
Have all his ventures fail'd? What, not one hit?
From Tripolis, from Mexico and England,
From Lisbon, Barbary and India?
And not one vessel 'scape the dreadful touch
Of merchant-marring rocks?
Not one, my lord.
It seems that Antonio has lost everything. Salarino then explains his friend's terrible dilemma. Shylock has claimed forfeiture since Antonio has missed the due date for the settlement of the bond. The money lender has stubbornly refused to accept any compensation afterwards, insisting on justice. It becomes apparent later, though, that Antonio has accepted his fate and has put himself at the mercy of the court, which is presided over by the duke.
After the trial, in which the decision goes against Shylock due to Portia's intelligent intervention, the parties return to Belmont where all are happy. At one point, Antonio makes the following remark when he addresses Portia:
Sweet lady, you have given me life and living;
For here I read for certain that my ships
Are safely come to road.
The reference to his ships is metaphorical. He is essentially thanking Portia for having saved his life and, therefore, restoring him to full health. It does not mean that his ships have returned safely. Portia has provided him with a lifeline and he can rebuild and restore his mercantile ventures.