We define a bona fide rough path solution for the Navier-Stokes equation with an additional rough transport term, and show that the SPDE on the three-dimensional torus driven by a fractional Brownian motion on H^\sigma has solutions characterised as the effective limits of a slow/fast system. We further show that this rough path solution is equivalent to the widely used incremental notion of solution (the unbounded rough driver formulation), demonstrating broader applicability to other nonlinear SPDEs.