Dissolved molybdenum (Mo) and uranium (U) concentrations were measured in five Indian estuaries; the Narmada, Tapi, Mandovi and the Mahi fall into the Arabian Sea and the Hooghly falling into the Bay of Bengal. Riverine Mo and U vary significantly, in the range of 1 to 90 and 0.02 to 19 nmol/kg respectively. The lowest Mo and U were observed in the Mandovi river, consistent with lateritic lithology exposed in its drainage, higher runoff and lower water-rock interaction. The Sabarmati has the highest U, 19 nmol/kg and sources from the groundwater having very high U concentration. The highest Mo (90 nmol/kg) is observed in the Mahi river and probably results from anthropogenic sources. Hooghly river seems to have high concentrations of Mo (14 nmol/kg) and U (8 nmol/kg) and are possibly derived from weathering of black shales of the Himalaya. Behaviour of Mo and U in all the estuaries analysed in this study is highly variable. Both Mo and U in the Narmada estuary during pre-monsoon and monsoon seasons and U in the Tapi estuary behave conservatively. Mo in the Tapi shows its addition in the mid salinity ranges (~ 4 to 12‰) and is sourced from anthropogenic activity probably related to effluent from industries situated along the estuary in this salinity range. Both dissolved Mo and U show their removal at lower salinity ranges in the Hooghly and the Mandovi estuaries. These estuaries are net sink of Mo in which significant amount of oceanic Mo along with riverine Mo is being lost. About 1.6 × 10 6 and 2 × 10 5 mol of Mo are being removed annually in the Hooghly and the Mandovi estuaries. Uranium removal is order of magnitude lower compared to Mo in both the Hooghly and the Mandovi estuaries. The loss of Mo and U in the estuaries are associated with mangrove swamps present in the estuaries which seems to be an important sink of the oceanic Mo and could represent its significant sink in oceanic budget of Mo. The Gulf of Cambay has high dissolved Mo concentration compared to that of global average seawater value which is attributed to its supply from anthropogenic sources. Industrial effluent waste waters along with polluted rivers supply ~ 5 × 10 6 mol of Mo annually to the Gulf of Cambay which could be derived from petrochemicals and pharmaceutical industries situated along the Gulf coast.