Safety is always the #1 priority and if you live in areas with sharks, gators or other confirmed dangers then never let your ego make you do something you shouldn't. Find the best and safest alternatives to the convenient ones. But for most of us the drama is in our heads, not the water.
You are the lurking creature. Fish, turtles and other water life are going to be more afraid of you (and the dozens of other triathletes) and will head in the opposite direction. Underwater plants and mud may be gross but they will be a non-factor when you start swimming. So quickly get in and get moving and you'll have less time to create worry in your mind.
Focus on what you can see. Visibility in lakes and oceans is usually poor to non-existent. And even if it was good, there won't be the friendly black line on the bottom. Yet this can all be overcome with a little practice and focus. There are three things you should look for: the target on the horizon (usually a buoy), a landmark on land and swimmers in front of you.
Getting used to poor visibility can be done in a pool too. Simply close your eyes when your face is in the water and open them when you turn to breathe. It will feel odd at first but will quickly become a rhythm you can be comfortable with.
Once you have some comfort with that, start to work on 'sighting': As you return your face to the water, glance up at the end of the pool. You only need to keep your eyes above the water line. Practice this every two to four strokes. Bonus: This will help strengthen your neck muscles which will help you be able to do this over a longer distance.
In open water, look for a landmark building, tower or tree to keep as your target and gauge for your line. During a race or training swim with others, follow the bubbles of the kicks in front of you but still use sighting with your landmark to ensure you are not taken off course by someone else.
If your concern has to do with not being able to see the bottom, just trust the fact that it's there and you don't need the bottom when you swim. You can always tread water or turn on your back if you need a break.
Acclimatize to the cold. There can be a very real physiological reaction to cold water swimming, even with a wetsuit. Your body will naturally tense up and your breathing can shorten and quicken. Overcome this by doing a proper warm up, splash water on your face or submerse yourself in it for a few seconds before swimming. Even taking cool-to-cold showers the few days beforehand can help you mentally and physically adapt more quickly.
While swimming, focus on taking slow, methodical breaths, this will override any tendency to breathe short and will help to relax all your muscles to swiftly get into your full pace and normal effort. You won't be cold forever so the sooner you get into the swim, the sooner you'll be able to adapt to the temperature and turn your thoughts to great technique.
As with everything, the more you practice, the better you'll get and the more confidence you'll have to just get out there and perform at your best.
Take your open water skills to your next triathlon.