Gone are the days where fresh, cold stream water was safe to drink. Today, there are many disease organisms contaminating fresh water streams due to improper disposal of human wastes including feces and also kitchen waste. Additionally, local wildlife is another common source of water contamination because they often defecate in or near the water.
Below is a LONG list of nasty organisms and bacteria that can be found in streams and other bodies of fresh water:
Protozoa, which also often come from human an animal feces:
and lets not forget helminth zoonoses such as:
Other water-borne diseases are cholera, botulism, typhoid, hepatitis A, dysentery, cryptosporidiosis, and polio.
It is generally not recommended to drink fresh water from streams. Hawaii is especially concerned about this. The state of Hawaii considers all fresh water from streams and rivers to be contaminated and does not recommend swimming in the ocean at the mouth of the stream. A major concern in Hawaii is Leptospirosis, a tropical bacterial disease that causes fever and other flu-like symptoms. It is spread through contaminated urine and is most commonly transmitted through fresh water.
For more on water-borne diseases, you can read previously asked GreenAnswers questions related this:
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