Surface nanostructure, either designed or generated as an artifact of the fabrication procedure, is known to influence interfacial phenomena intriguingly. While surface roughness-wettability coupling over nanometer scales has been addressed to some extent, the explicit interplay of hydrodynamics and confinement toward dictating the underlying characteristics for practically :f relevant material interfaces remains unexplored. Here, we bring out unique roles of surface nanostructures toward altering flow of water in a copper nanochannel, by capturing an exclusive interplay of confinement, roughness, wettability and flow dynamics. Toward this, non-equilibrium molecular dynamics (NEMD) simulations are performed to examine the effect of nanoscale triangular roughness. The width and height of the triangular microgroove are varied along with different driving forces at the channel inlet, and the results are compared with those corresponding to smooth-walled nanochannels. We also unveil the nontrivial characteristics of the interfacial topology as a consequence of spontaneous phase separation at the fluid-solid interface. For a constant driving force, we show that the interface may exhibit concave or convex topology, depending on the nanogroove geometry. Our results provide new vistas on how designed nanoscale roughness structures can be harnessed toward controlling the transport of water in a practically engineered nanosystem, as demanded by the specific application on hand.