Brussels is connected to the sea by canals, but only river boats are small enough to dock at the ports of Heembeekkaai or Becodock. From Becodock, which is near Yser train station, you can walk to the city center, though from Heembekkai it is better to take a bus. There is nothing of interest for river-cruise passengers at either port.
Large cruise ships dock in Antwerp or Zeebrugge. Trains run from both cities into Brussels.