When you sell Plunder Goods at Port Cities, your Ship(s) will return with Silver as profit from trading.

The Silver from selling the Plunder Goods will be added to your Depot upon arrival at your Territory.

Also, you can only receive as much Silver as you can store,

which means that if you make more Silver than you can store in your Depot, your surplus Silver will disappear.

You can either upgrade your Depot before your ship arrives so you can store more Silver, 

or you can use your Silver to make room.