The general reasoning given for the act; throwing coins into a River is that it brings Good Luck. However, scientifically speaking, in earlier times when civilization was booming in India their main need resource was water and it was mainly used for agriculture, cooking, drinking, etc. so they have to stay near water places like lakes, rivers etc, so their way of using copper was for attracting dirt to purify water and also used in trading purposes so most of the currency used was made of copper unlike the stainless steel coins as of today. 
As said Copper is a vital metal very useful to the human body and used to attracting dirt as it is mentioned in Ayurveda that it purifies water. Water was Stored in Copper pots which Kills Contaminating Diarrhoeagenic Bacteria and, thus in temples also priests use copper vessels to give thirtha/holy water.