Need help with invasive water plants and water quality in pond.

Hi there! Recently I started taking care of my parents' land and they have a medium-sized pond that they would like to "clean up" and eventually be able to swim in but I'm not familiar with this type of thing and need some help in getting rid of some invasive water plants as well as improve the quality of the water in general, if possible. Their well is situated on the outskirts of the pond closer to the road and didn't want to have anything I do to the pond affect the water source they use for their home.

Their neighborhood is in the foothills (oak woodland) of the Sierra Nevada at approximately 1,450 feet in elevation. There is a series of 3 ponds almost equal in size that sit on a seasonal creek and theirs is the third. I believe all 3 ponds are manmade though the creek itself is natural. I've attached pictures to help draw a picture of what I'm working with here. It would be nice if it could be kept as natural as possible, but I am open-minded. Preferably, I don't want to mess with the wildlife inhabiting the pond too much. Despite it being how it is, there's still quite a few species that thrive there.

Is there a way to scrape the water plants out? Is there any native plants/animals I could introduce that could help with water quality? Not sure exactly what to do, these are just some thoughts I've had. Any advice would be greatly appreciated! :)

Water plants are excellent mulch and compost ingredients or worm food.  You can just gently rake them out every now and then.  The problem is the solution.

If you want aquatic plants gone for good, you need to really redig the pond (a machine type of fix). What happens is, if the sides are not steep enough, light penetrates through the water to the soil and stimulates the plant growth. If you make the sides deeper, this is greatly reduced and you will not get aquatic plants.

I fully recognize that it is not an easy to do fix however.

I'm no pond expert, so this is just me as 'keyboard consultant' but couple things-

Are you saying the pond you are working on is the THIRD in line, as in the last down-stream one?   That stuff from the creek and the other 2 ponds flow into yours?     That will probably end up messing up your long term solution, as whatever is in those upper ponds will flow into yours.

Where else does that creek wander through upstream from you?   Again, no expert, but that water quality reminds me of creeks from back in Wisconsin that wandered through farms with dairy cattle - that is, that algae there looks "powered" by nitrogen runoff - from cow poop or field fertilizer.   I would want to think about what level of exposure you're comfortable with if that's the case.

I agree with other answer about how great that stuff would be to gather and add to compost or garden.  

Perhaps, if I'm in the ballpark about the nitrogen content, you could plant something - at the upper end edge -  that really sucks up nitrogen. Something you'd like, and could use.  I don't know what that would be, but maybe bamboo?  

What sort of wildlife is in the pond now?  Are there fish? frogs? how deep is it?