How do I figure out the biological diversity of aquatic environments?

Answer 1

By getting very wet and muddy and having water fights. Well, that's the way we did it.

Basically select a suitable site and go and study it. You may simply want to stand and observe what you see of you can use underwater cameras, take samples back to a lab for microscopic examination, or catch the aquatic life by netting or trawling your chosen area. You may want to consider examining the life found in the sediment as well (if it applies).

A lot depends on the type of site in question. What you'll find and how you'd study a stream and it's banks is very different from the approach to studying the deep ocean.