Quantifying the concentration of dissolved nutrients in water is traditionally achieved by spot sampling and subsequent laboratory analysis. The process is manually intensive and intrinsically limits the frequency and/or number of data points that can be obtained therefore the short-lived episodic events could be missed. By using sensors to monitor in situ, however, much larger data sets can be obtained which can be reported in real-time and with less overall capital expenditure. The majority of current commercial ammonium sensors are based on ion-selective electrodes, produced for example by Xylem YSI and RSHydro. These are user-friendly and feature high measurement frequencies but, as is commonly found for electrochemical-based sensors, their calibration drifts over time requiring frequent manual recalibration. Moreover, they have also been shown to be highly susceptible to interference from changes in ionic concentration. We report here the development of a novel droplet microfluidics based ammonium sensor, and its deployment to a sequential batch bioreactor enriched with polyhydroxyalkanoates (PHAs) accumulating bacteria. PHAs are microbially produced polyesters which are biodegradable, biocompatible, and have tuneable mechanical and thermal properties and their microbial production has garnered vast research interest [1]. The sensor miniaturizes the widely adopted indophenol blue method in droplets (LOD of 0.11 mg/L), can perform high frequency and accurate measurement and provide long period of monitoring with minimal reagent consumption (1700 nL per analysis). Driven by a specially designed persistaltic pump based on a phased-flow droplet generation method [2], the sensor can autonomously collect samples (via filter) from the bioreactor, produce droplet trains, regulate temperature for completion of reaction and provide colorimetric measurements (5 per minute) via an inline spectrophotometer, thus removing human intervention. The preliminary data obtained over a four day period shows high resolution monitoring and reveals the fast feeding behavior of the bacteria, which could lead to the design of more efficient bioreactors and feedback controlled bioprocessing. These type of sensors could form the next generation of in situ sensors, to address wide applications in monitoring for wastewater treatment, environmental monitoring, aquaculture and others, especially when transient and episodic events are involved.