You should show some examples and tell us what film you've used (50,100,200,400,800 ASA etc.). The visibility is also an interesting point. You should always almost use the internal strobe.
In most cases you should uses 100/200 ASA films. The results with the build in strobe are not perfect because in most cases you will see reflections at your picture.
At shallow water you can try to take photos without the build in strobe.
I'am not an owner of MX-5 but I've seen lot of nice pictures taken with MX-5 at very bad circumstances, so I believe you should be able to get some results. Not professional quality but something usesfull.
Another hint:
Try to take your photos always from button to surface (fishes, divers, wrecks). Then your camera is able to use all the light available.