Hello Mr. Prasad, you have raised a very crucial issue . Yes, ground water resources in several areas of the country are getting polluted due to over application of fertilizers and pesticides, indiscriminate disposal of effluents from industries and urban sewerage.
As here we are focused on artificial recharge wells, i must add that generally soil strata works as a primary filter for the water. But if the water is highly contaminated then soil strata can not do any wonder. We should avoid direct inject of industrial used water, road runoff, sewage water etc . But if this is the only source for ground water recharge then the water should be treated first according to the local water standards. How about first constructing settling tanks, buffering waterways etc?
You have mentioned about the pits in cities, I am sure they are constructed without considering soil conditions and soil texture type. These types of poorly constructed pits are not solving any problems but contaminating the ground water.
Indian govt. Now a days putting lots of affords in research and studies about ground water. Hope, we will stop this contamination of ground water by constructing all the recharge well scientifically not just by digging them to increase the number.