An essential approach for in vivo chemical monitoring is to use sampling probes coupled with analytical methods; however, this method traditionally has limited spatial and temporal resolution. To address this problem, we developed an analytical system that combines microfabricated push-pull sampling probes with droplet-based microfluidics. The microfabricated probe provides spatial resolution approximately 1000-fold better than that of common microdialysis probes. Microfabrication also facilitated integration of an extra channel into the probe for microinjection. We created microfluidic devices and interfaces that allowed manipulation of nanoliter droplet samples collected from the microfabricated probe at intervals of a few seconds. Use of droplet-based microfluidics prevented broadening of collected zones, yielding 6 s temporal resolution at 100 nL/min perfusion rates. Resulting droplets were analyzed by direct infusion nanoelectrospray ionization (nESI) mass spectrometry for simultaneous determination of glutamine, glutamate, γ-aminobutyric acid, and acetylcholine. Use of low infusion rates that enabled nESI (50 nL/min) was critical to allowing detection in the complex samples. Addition of 13C-labeled internal standards to the droplet samples was used for improved quantification. Utility of the overall system was demonstrated by monitoring dynamic chemical changes evoked by microinjection of high potassium concentrations into the brain of live rats. The results showed stimulated neurochemical release with rise times of 15 s. This work demonstrates the potential of coupling microfabricated sampling probes to droplet-based mass spectrometric assays for studying chemical dynamics in a complex microenvironment at high spatiotemporal resolution.