For several applications there are advantages in writing turbulent flow equations in a coordinate frame aligned with the streamlines and several two-dimensional examples of this approach have appeared in the literature. In this paper, we extend this approach to general three-dimensional flows. We find that, in any flow that has a component of its vorticity aligned in the streamline direction, congruences of its streamlines do not form integrable manifolds. This limits the development of a streamline coordinate description of such flows, although some useful results can still be obtained. However, in the case of general three-dimensional complex-lamellar flows, where the mean velocity and mean vorticity are everywhere orthogonal, a complete streamline coordinate description can be derived. Furthermore, we show that general complex-lamellar flows are a good approximation to boundary layers and thin free shear layers. We derive the underlying true coordinate system for such flows, where the orthogonal coordinate surfaces are two stream surfaces and a modified potential surface. From this we obtain physical equations, where flow variables have the same dimensions they would have in a Cartesian coordinate frame. Finally, we show that rational approximations to these equations, which describe small-perturbation flows, contain some terms that have been ignored in previous applications and we detail some practical applications of the theory in modelling and analysis.