In numerous industrial processes involving fluids, viscosity is a determinant factor for reaction rates, flows, drying, mixing, etc. Its importance is even more determinant for phenomena observed are at the micro-and nano-scales as in nanopores or in micro and nanochannels for instance. However, despite notable progresses of the techniques used in microrheology in recent years, the quantification, mapping and study of viscosity at small scales remains challenging. Fluorescent molecular rotors are molecules whose fluorescence properties are sensitive to local viscosity: they thus allow to obtain viscosity maps by using fluorescence microscopes. While they are well-known as contrast agents in bioimaging, their use for quantitative measurements remains scarce. This paper is devoted to the use of such molecules to perform quantitative, in situ and local measurements of viscosity in heterogeneous microfluidic flows. The technique is first validated in the well-controlled situation of a microfluidic co-flow, where two streams mix through transverse diffusion. Then, a more complex situation of mixing in passive micromixers is considered and mixing efficiency is characterized and quantified. The methodology developed in this study thus opens a new path for flow characterization in confined, heterogeneous and complex systems.he methodology developed in this study thus opens a new path for flow characterization in confined, heterogeneous micro-and nano-systems.