what is the depth you are targeting. There are couple of UAVs available.

It will be a good way of utilizing UAVs (sort of a secondary objective), but then the camera types might have to be adapted for that additional data acquisition. What are the types of cameras in use right now? do UAV's have active radar or Lidar....of course the decision will have to be taken with costs in mind as well as area of interest (If the UAVs flight route has to be modified or not).

To answer this question, you need to define your target as specifically as possible.  "Mapping emergent and submerged" vegetation is not specific enough to provide a suitable answer to the question you raised.  What is the area of your target region for mapping?  What kind of data do you intend to collect to answer the specific questions you have regarding the wetland vegetation?  Visible spectrum, infrared, multispectral, hyperspectral, LiDAR, etc. all would provide data that could be used for wetland mapping, but you must specify your research question from the very beginning to select the correct sensor to provide your intended results.  What kind of resolution do you need to answer your mapping question?  Will community-level plant resolution be sufficient, or do you need resolution at the individual stem level?  Once you have identified a sensor that meets your goals, (and one that you can afford), then you should find an airframe that is capable of getting your sensor over the target, and then pursue the legal hurdles to conducting your flights once you have an airframe and sensor package selected.  Your question to ResearchGate is currently too broad to answer.  If you define your research question more clearly, then we can help provide you with information tailored to your specific mission(s).

Define your target first

But mostly use a quadcopter if your area is not very large

U can use any type

But my recommendation is a quadcopter

Dear Victor,

You have to specify the required bands, area (how big) and resolution. Then, choose the best available drone or sensor!

Best of luck.