If a Jewish couple had to spend an extended period of time (6 months) in an isolated location (desert island, several miles off civilized coast). Could the woman do her Mikvah in a natural pond or would it be better to abstain?

Shalom U'verachah, One is allowed to use the sea or certain types of natural spring pools as a Mikvah. However in order to do so one needs to be careful, and knowledgable, of many specific halachot. First, it must be clear that the pool water comes from a spring source and not from another source. There must be sufficient volume of water, and it must be in place where the woman can immerse herself without others seeing her and where she will feel comfortable and not rush the immersion and maybe do so in an inappropriate way. She must ensure that all her hair and body enters the water at the same time. I suggest that if this is a practical question you learn the appropriate Halachot before travelling to make sure that you know what you are doing and can consult with a Rav if neccesary. Kol Tuv