River Yamuna is one of the most sacred major tributaries of river Ganga. This study aimed to assess the level of heavy metals in monsoon and non-monsoon season in river Yamuna in Uttar Pradesh, India and to assess the possible source of contamination and its associated health risk. Except for iron (Fe), the mean levels of all metals were within drinking water safe limits in both seasons. Except for chromium (Cr), lower values were observed for other metals in the monsoon season could be attributed dilution effect. Multivariate analysis indicated that both geogenic and anthropogenic sources contribute to heavy metals in river Yamuna in monsoon and non-monsoon seasons. The health risk in terms of hazard index (HI) and fuzzy-logic hazard index (FHI) demonstrated that both HI and FHI values among children exceeded the safe limit in most of the sites in non-monsoon seasons and in few in monsoon season. For adults, HI and FHI values were within safe limit.