Holy River Yamuna is the largest river and main source of water for the various cities is getting highly polluted due to heavy discharge of sewage and industrial effluents, containing heavy metals, into surface water as a result of rapid urbanization, industrialisation and population growth. The major objective of this research was to take an in-depth analysis of water quality and heavy metal pollution of Yamuna River in different areas of Agra city during pre and post-rainy season. The analytical results show that Zn and Cu metals are within the permissible limit but the concentration of Fe, Zn, Cr and Mn increased in post rainy season. It was also analysed that the concentration of Cr may be higher due to existence of various leather industries in the Agra city. It was noted that water quality of Taj Ganj area was highly alarming with respect to other parts.