This paper reports an experimental characterization of a simple method for rapid formation of droplets, or plugs, of multiple aqueous reagents without bringing reagents into contact prior to mixing. Droplet-based microfluidics offers a simple method of achieving rapid mixing and transport with no dispersion. In addition, this paper shows that organic dyes at high concentrations should not be used for the visualization of flow patterns and mixing of aqueous plugs in multiphase flows in this system (fluorinated carrier fluid and PDMS microchannels). It reports an inorganic dye that can be used instead. This work focuses on mixing in plugs moving through straight channels. It demonstrates that, when traveling through straight microchannels, mixing within plugs by steady recirculating flow is highly sensitive to the initial distribution of the aqueous reagents established by the eddy flow at the tip of the forming plug (twirling). The results also show how plugs with proper distribution of the aqueous reagents could be formed in order to achieve optimal mixing of the reagents in this system.