Okay, now that we have our lines, we need to get some colour down. In this case there are four different coloured areas - the sea, the deck, the sails and the rocks. First things first - create four new transparent layers and name them for the colours they will hold.
We'll start with the sea colours. We could just do a block fill of a nice sea colour to start with, but that's a bit dull. It's more interesting if we can get a bit of variation in the colour for the sea, so we will build it up bit by bit.
For varying colours I find it useful to use the airbrush with the 'Use colour from gradient' switch turned on. Gimp comes with a deep-sea gradient so that seemed particularly appropriate for this case but you can use others, or make your own. In this case I use the following settings:
Now take a large fuzzy brush and block in the sea with colour. Note that I have scaled up the brush to aid in quickly filling a large area. Don't worry if it's not smooth at this stage. We'll deal with that in a minute. Also, don't worry if the colours aren't quite right. They are just going to give us a starting point. Finally, the edges are also not a great problem. It is more important to get the colour up to the edges of the area you are filling in than worry about going over into the adjoining area.
The end result will look blotchy and non-too smooth. Switch from the airbrush tool to the smudge tool. Now I decided that I wanted it to look as if the waves were rolling in from the north-east. Therefore I use the smudge tool to blur the colours in lines from north-west to south-east. Here is a screenshot of the smoothing in progress. Note that the area in the bottom right of the image has not been smoothed yet.
Notice how the colour variation smooths out to give the impression of waves. Now this still looks a bit lurid. I'll deal with that next.