Water is usually the transmitter of protozoa (amoebic) infections, but that does not mean that you could not have contracted a worm or fluke.
Some of the protozoa are self-limiting meaning they will pass as the immune system can overcome. Some are more resistant such as blastocystis hominis or b. hominis. If this is the case then it would be best to review badbugs.org.
Proper testing is the method before treating, Metametrix stool test is best and the only one who gives consisent results.
You could try to treat with some finely minced garlic, neem, cats claw and a herbal formula such as ParaCleanse from Banyan's or other similar products. See where you get with that.