When most people think about underwater dangers they have a vision of a large shark or predator animal, when in fact the danger faced by these animals can be less of a risk than some other rarely though of dangers.
Currents - be sure that you are aware of the currents that exist in the area. Also consider the timing of the tide, as some dives will be safer and more enjoyable at certain times of the tide.
Good Visibility - I bet you are thinking how this could possibly be a danger. As visibility increases we can easily descend beyond our planned dive depth. We can also swim a lot further in a shorter period of time, simply because we can see more. Take note of your gauges in good visibility.
Exposure - affects scuba divers no matter where you dive, as you can be affected by exposure to the cold water and suffer from hypothermia. On the other end of the scale when diving in tropical waters, we can also become complacent with protecting our skin both in an out of the water. Try to match the thickness of wetsuit to the location you are diving
Creatures - these can include the obvious one of sharks, crocodiles, barracuda, moray eels and sea snakes. Most of these creatures are not likely to attack you unless provoked. In the situation of the shark, a common rule is that if the shark is bigger than you get out of the water. My fear is by far more of the crocodile and I think if I was to see one in the water, it would be a race to get to the boat. Remember that as a scuba diver you have control over your buoyancy in the water, and this gives you the ability to keep a close eye on the creature in question.
Corals - although many corals can give you a nasty scratch and if you touch the fire coral be prepared for a strong stinging sensation, most corals suffer far more threat from fisherman, divers and anyone else who come into their backyards. Take only pictures and leave only footprints, is a good motto.