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Abstract The pattern of N/P/Si stoichiometry, although an important driver regulating river ecology, has received limited research attention for Ganga River. We investigated shifts in N/P/Si stoichiometry and ecological nutrient limitation as influenced by Varanasi urban core along a 37-km-long stretch of Ganga River. We also assessed the trophic status of the river in relation to shifting elemental stoichiometry. Together with point sources, atmospheric deposition coupled surface runoff appeared important factors leading to N/P/Si stoichiometric imbalances along the study stretch. The N/P and Si/P ratios declined downstream from 15.5 to 6.5 and 15.7 to 4.4, respectively, whereas N/Si increased from 1.01 to 1.6. Significant negative correlation of N/Si with biogenic silica to chlorophyll a (Chl a) ratios, and biogenic silica to phycocyanin ratios indicated increased growth of non-siliceous algae downstream signifying N and Si limitation with possible implications on food-web dynamics and feedback processes in the river in long run.