I used to judge these science projects for high schools and I'm a fan of Steve's idea about global warming and its affect on coral growth, viability, etc. This has mainstream ecological significance and judges are always looking for something that is both visually appealing (as there's also local area science project competitions beyond the school -although I'm not sure for elementary/middle schools) and addresses global issues. Dan does have a point with long term temperature differences affecting reefs over-time and that it may scream "my parents did my experiment". During my graduate school days, I had friends in our PhD program that were looking at long-term biodiversity in reefs and rainforests with respect to global warming or habitat change, and this was a 6-8 year endeavor. But honestly, the majority of the great science projects from 6th graders required adult help and supervision. It wasn't until the high school science projects that I had students contacting us to join our lab for a short period of time to conduct research on our cancer cells, in which case, their parents were not around.
To limit the "my parents did my experiment" syndrome, I suggests helping him choose a topic (i.e. coral bleaching commonly observed in acros, coral growth...) and reading books and such on the topic. If he's interested in the topic in terms of temperature or light intensity, have him come up with a hypothesis on his own and write it down (e.g. Null Hypothesis: temperature has no effect on coral growth/bleaching). And even if his hypothesis is wrong (e.g. Hypothesis: corals will bleach at lower temperatures compared to high temperatures), it doesn't matter. As hard as it may be, don't change his hypothesis! His job now is to test whether his hypothesis is rejected/accepted, and he can say so on his report. And the experiment can be as complicated (looking & measuring biodiversity by providing several types of coral for each condition and having him count the number of corals that died or measure the total weight overtime) or as simplistic as he wants and as much money you're willing to give him. Not sure how much time he has, but he can setup a simultaneous short- and long-term study where one tank has temperature graduations that were 3 degrees apart and the other tank 6 degrees apart. He may observe small changes but over a longer period of time in the long-term tank and may see coral bleaching overnight in the short-term tank. Either way, he can have a lot of fun with this and who knows...he may want to become a scientist one day.