Can one player put more than one of his agents at Waterdeep Harbor?
Yes, you can place more than one of your agents at Waterdeep Harbor to play multiple Intrigue cards. At the end of the round, the agents there are placed onto other spaces in order, regardless of who they belong to.

On Page 9 of the rulebook (emphasis mine):


  Waterdeep Harbor has three action spaces instead of the usual one. You can assign more than 1 of your Agents to Waterdeep Harbor if it still has an open action space (but you still can't assign more than 1 Agent per turn).