Human-induced N:P:Si imbalances and associated shifts in nutrient limitation in Ganga River remain relatively uncertain despite recent studies highlighting its importance. The goal of this watershed-scale study was to investigate the nutrient-limiting status of Ganga River, as influenced by atmospheric deposition (AD) and catchment runoff together with urban-industrial development. AD was highest in middle watershed, where AD of NO_3^- ranged from 10.56 to 28.93, AD of NH_4^+ from 4.26 to 15.42, and AD of PO_4^(3-) from 1.82 to 2.94 kg ha^(-1) year^(-1). The results showed that AD-coupled catchment runoff is an important factor, in addition to direct urban-industrial release, causing N:P:Si imbalances that lead to N over P limitation (N:P < 16:1) and Si over N limitation (Si:N < 1) in the river. The skewed N:P:Si ratios observed here may have important effects on phytoplankton/diatom growth and trophic cascades and consequently on river ecology. This study that forms the first report on changing atmosphere-land-water N:P:Si linkages suggests that the current policy on Ganga rejuvenation needs to focus more strongly on cross-domain drivers of stoichiometric imbalances and approaches to minimize them.