One and a half-year-old Deepti and 6-year-old Guddi died after falling ill.
85 more children have taken ill after consuming contaminated water, Chief Medical officer Nepal Singh said.
Over 150 residents of Ankur Village, situated on the Mathura-Vrindavan road, have been hospitalised for vomiting and showing symptoms of diarrhoea.
"Water being supplied to the village passes a cow ranch and due to breakage in the pipeline, the water got polluted with accumalated dung waste," Singh said.
Singh said the matter will be probed.