Here the double meaning is the sea of life. Fenerty wrote:

Hence Christian learn when tossed and driven
O’er life’s tempestuous sea,
The saviour from his throne in Heaven
Can calm its storms for thee.

The first eight stanzas are basically the boat sets sail, port is out of sight, a storm develops, too late to turn back, storm gets worse, the boat is out of control, high waves, waves of water falling on them. This is analogous to how life begins for each of us, and more so when efforting towards a goal. As that big wave of water falls straight for us, there looks like little hope. And even when hope appears, it is easily doubted.