The water-induced crystallization of alkylbenzenesulfonate-coated amorphous calcium carbonate (ACC) nanoparticles in water-in-isooctane sodium bis(2-ethylhexyl)sulfosuccinate (NaAOT) micro emulsions at a [H2O]/[NaAOT] molar ratio (w) of 10:1 produces a range of organized hybrid surfactant-vaterite nanostructures depending on the water droplet/ACC nanoparticle number ratio, n = [H2O]/[CaCO3]. The. crystalline nanostructures develop within primary aggregates of the surfactant-stabilized ACC nanoparticles by in situ mesoscale transformation, which is mediated by the extent of coupling at the surfactant-inorganic interface. Strong coupling in the presence of low amounts of water (n = 34) gives monodisperse spheroidal aggregates of densely packed 5 nm diameter surfactant-coated vaterite nanoparticles, whereas weak interactions at n = 3400 produce discrete vaterite nanoparticles, 130 nm in size. Significantly, intermediate levels of coupling produce anisotropic nanostructures such as spindle-shaped aggregates of 18 nm sized surfactant-coated vaterite nanoparticles (n = 170) and high-aspect-ratio bundles of co-aligned 10 nm wide twisted vaterite nanofilaments (n = 340). Adding excess aqueous CO32- to the microemulsion droplets inhibits the growth of the nanofilaments, whereas excess Ca2+ has no effect. The results show that the transformation pathways are determined by the extent of water penetration into the ACC cores and electrostatic interactions at the mineral-surfactant interface, and indicate that complex hybrid nanostructures can be assembled in situ when these processes are coupled synergistically at the mesoscopic level. Such observations could be of generic importance in nanochemistry and biomineralization.