Flood-tide below me! I watch you, face to face; Clouds of the west! sun there half an hour high! I see you also face to face.
From his vantage point on the ferry, the speaker addresses the water that is rushing by below him. The tide is coming in, so it's a "flood-tide."
Summoning his best Robert De Niro, he looks at the water and says, "You! Yeah, you!" – (makes the "I'm watching you" motion with his fingers) – "That's right. I'm watching you!"
The water is personified with a "face," as are the "clouds" and the "sun" that he sees reflected there.
It's a half an hour from sunset, and the sun sets in the west, which is why he notices the "clouds of the west."
As you'll discover in this poem, Whitman is a very confrontational poet, though not in an aggressive way. He's all about eye contact. As they say on Seinfeld, he's a "close talker."