Ionic liquid/water binary mixtures are rapidly gaining popularity as solvents for dissolution of cellulose, nucleobases, and other poorly water-soluble biomolecules. Hence, several studies have focused on measuring the thermophysical properties of these versatile mixtures. Among these, 1-ethyl-3-methylimidazolium ([emim]) cation-based ILs containing different anions exhibit unique density behaviours upon addition of water. While [emim][acetate]/water binary mixtures display an unusual rise in density with the addition of low-to-moderate amounts of water, those containing the [trifluoroacetate] ([Tfa]) anion display a sluggish decrease in density. The density of [emim][tetrafluoroborate] ([emim][BF₄])/water mixtures, on the other hand, declines rapidly in close accordance with the experimental reports. Here, we unravel the structural basis underlying this unique density behavior of [emim]-based IL/water mixtures using all-atom molecular dynamics (MD) simulations. The results revealed that the distinct nature of anion–water hydrogen bonded networks in the three systems was a key in modulating the observed unique density behaviour. Vast expanses of uninterrupted anion–water–anion H-bonded stretches, denoted here as anion–water wires, induced significant structuring in [emim][Ac]/water mixtures that resulted in the density rise. Conversely, the presence of intermittent large water clusters disintegrated the anion–water wires in [emim][Tfa]/water and [emim][BF₄]/water mixtures to cause a monotonic density decrease. The differential nanostructuring affected the dynamics of the solutions proportionately, with the H-bond making and breaking dynamics found to be greatly retarded in [emim][Ac]/water mixtures, while it exhibited a faster relaxation in the other two binary solutions.