In the present paper we study slow-fast systems of coupled equations from fluid dynamics, where the fast component is perturbed by additive noise. We prove that, under a suitable limit of infinite separation of scales, the slow component of the system converges in law to a solution of the initial equation perturbed with transport noise, and subject to the influence of an additional Itō-Stokes drift. The obtained limit equation is very similar to turbulent models derived heuristically. Our results apply to the Navier-Stokes equations in dimension d=2,3; the Surface Quasi-Geostrophic equations in dimension d=2; and the Primitive equations in dimension d=2,3
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