Some folks had mentioned that they liked my water texture in my latest maps so I thought I'd do a little tutorial on how I made them. I don't use a standard texture, I create a custom water effect to suit each map. It takes a little practice to get looking good but the end result can be really good.
Create a new layer and completely fill with a mid-range blue [menu:edit/fill]. The layer needs to be completely filled to stop the filter making transparent gaps at the edges.
Then draw in roughly the position of the intended river, sea or lake on the map some variations of blue colour with a softish brush (see the pic below for an idea).
Apply quite a strong gaussian blur to even the colours out [menu:filter/blur/gaussian blur].
Next open the Ocean Ripple filter [menu:filter/distort/ocean ripple] and choose settings that suit the water surface you are seeking. I find a small ripple size and high magnitude works well for large scale maps. The glass filter (set on frost) can also give good results - experiment!
Apply a mask to the layer to hide the parts of the layer that you don't want to see. Do this by making sure the water layer is current and clicking [menu:layer/add layer mask/hide all]. The water layer should vanish, don't panic it's hidden by a complete mask. The underlying layers should be visible if there are any.
Click in the new mask thumbnail in the layers palette (it'll look like a black square to the right of the pattern symbol) to make the mask active. Use a white soft brush to draw the extent of the water. Use a low flow value to draw the edges for a natural water line.
Un-link the mask and the water layer (by clicking the little chain between the pattern and the mask thumbnails) and move the water effect around in your mask to get the best view of the ripples [hotkey 'v' = move].
Insert a hue and saturation adjustment layer [menu:layer/new adjustment layer/hue and saturation] click OK on the next two dialogue boxes. Group with the water layer by alt-clicking between the new adjustment layer and the water layer. This means the adjustment layer only affects the layer it is linked with.
Double click the adjustment layer thumbnail (the left one, not the mask) to open the adjustment dialogue box. Reduce the saturation for a more realistic effect for standard water. Change the hue if you want mud, swamp, etc. and you're done!
Not sure if these filters are available in GIMP but if you've got photoshop it's easy.
[Edit - made the tutorial a little easier to follow for photoshop novices]