Conjunction of miniature nanosensors and droplet-based microfluidic systems conceptually opens a new route towards sensitive, optics-less analysis of biochemical processes with high throughput, where single device can be employed for probing of thousands independent reactors. Here we combine droplet microfluidics with the compact silicon nanowire based field effect transistor (SiNW FET) for in-flow electrical detection of aqueous droplets one by one. We chemically probe the content of numerous droplets as independent events, and resolve the pH values and ionic strengths of the encapsulated solution, resulting in a change of the source-drain current ISD through the nanowires. Further, we discuss the specificities of emulsion sensing using ion sensitive FETs and study the effect of droplet sizes with respect to the sensor area, as well as its role on the ability to sense the interior of the aqueous reservoir. Finally, we demonstrate the capability of the novel droplets based nanowire platform for a bioassay applications, and carry out a glucose oxidase (GOx) enzymatic test for glucose detection, providing also the reference readout with an integrated parallel optical detector.