What role have nitrates and phosphates played in damaging Muddy Creek?

Nitrates and phosphates lead to eutrophication and anoxia in the creek which caused aquatic animals to die and damaged the creek.

Explanation:

Nitrates (NO3-) are chemical compounds that contain nitrogen and oxygen molecules. They are salts that are commonly found in fertilizers and are soluble in water. Phosphates are also compounds that are used in agricultural processes.

Nitrates and phosphate found in water are usually from plants that  have been washed off by rain water and also from vehicles' exhaust.

When there are abnormally high levels of nitrates and phosphates in water, it becomes difficult for aquatic animals to survive. In bodies of water, the nitrates and phosphates become sources of food to algae and other plants, this causes them to become over stimulated, and lead to Eutrophication (a high concentration of nutrients) and Anoxia (lack of oxygen).

This causes the fishes to run out of oxygen and die. Then the water begins to change color (milky white or green), give off an offensive odor and gradually turns into a  swamp and eventually a meadow

the answer will be a) proteins i believe

yes, because even though a theory has a  lot of evidence to support it, it is not always true