Dropping of puja items in a river is a very old tradition when all the puja items used in a Hindu puja were made of natural materials. Rituals and pujas are performed by a devotee to fulfill certain wishes. As per Hindu Holy Scriptures, water is one of the manifest forms of the Supreme Being (God). It is also said in the Rig Veda that in the beginning there was only Water. So when the devotee offers the puja items to water the devotee feels that it is directly offered to the Supreme Truth.
Dropping of puja items in rivers should not be practiced anymore as majority of puja items are not natural products. Most of the Hindu puja items today contain plastic and numerous other non-degradable materials. Rivers in olden days were free flowing and therefore what was offered was immediately carried away and there was no stagnation.
It must be noted that several rituals and practices in Hinduism were started more than 5000 years ago. In ancient days, only natural materials were offered to Hindu gods and goddesses. Even fifty years ago our elders used to make sure that only natural products were used in pujas. But things have changed now and people only use readymade products and majority of them are unnatural.
As we no longer perform pujas as per tradition, we should not be adamant in throwing of puja materials in a water body. The best option is to reuse the non-degradable puja materials.