The general reasoning given for this act by most of the people today is that “It brings Good Luck”.

Storing water in copper and silver pots finds mention in ancient texts of Ayurveda for purification of water.
Throwing copper coins in the holy rivers was one of the ways our fore-fathers made to ensure us 99.9% infection free water, As rivers were the Main source of drinking water. Making it a custom ensured that all of us follow the practice. If coins remain in rivers for a long time then it becomes beneficial for those who drink it.
More over, i think you would like to know that these days some countries are equipping metro trains with copper to make them anti-microbial. See, how other countries are researching and realizing the facts and how we are neglecting everything just because it is a part of our custom.
Throwing of coins into times and water stream In the ancient times majority of the civilizations settled near a water source as it is one of the main components for the survival of humans. This is the reason why in all the ancient texts rivers are co sidered to be as mothers as they used to help a civilization sustain food. After the discovery of the use of copper the civilizations started using the same for making their uteinsell and currency.
However apart from this our sages also discovered the benifit of copper in the human body and it’s anti bacterial properties. Since in those periods copper was not found in enough quantity in foods sages invented the other source which so far has been helping the civilization to prosper – Water. So they started immersing the copper in rivers so that the water absorbs the copper and in turn harmful bacteria gets eliminated and humans also get enough copper while in taking the water. This is also one of the reasons why brass utensils were used as they too contain copper and water stored in them or food cooked in such utensils absorb copper. However now days we do get copper through many sources but the practice is still followed as some of the great practices if our cultures cannot be discontinued. Instead of throwing coins (now days which does not contain copper) it’s better we get small copper pieces and use then and play our part in keeping the environment clean.