This work features the base-promoted on-water synthesis of [1,6]-naphthyridines from methyl ketones, malononitrile and phenols or thiols. The reaction conditions were carefully tuned to drive the product selectivity from 3H-pyrroles to [1,6]-naphthyridines. The advantages of this method lie in its simplicity, cost effectiveness, and environmental friendliness, representing a new effort toward the on-water synthesis of [1,6]-naphthyridines without starting from a nitrogen-containing heterocycle and highlighting the versatility of the nitrile functional group.