Microfluidics is one of the most fascinating fields that researchers have been trying to apply in a large number of scientific disciplines over the past two decades. Among them, the discipline of food and pharmaceutical formulation encountered several obstacles when combining microfluidics with aqueous media. Indeed, the physical properties of liquids at micrometric volumes being particular, the droplet generation within microfluidic devices is a big challenge to be met. This focus review is intended to be an initiation for those who would like to generate microdroplets in microfluidic systems involving aqueous continuous phases. It provides a state-of-the-art look at such systems while focusing on the microfluidic devices used, their applications to form a wide variety of emulsions and particles, and the key role held by the interface between the device channels and the emulsion. This review also leads to reflections on new materials that can be used in microfluidic systems with aqueous continuous phases.