Sensors based on single-walled carbon nanotubes (SWNT) are integrated into a microfluidic system outfitted with data processing and wireless transmission capability. The sensors combine the sensitivity, specificity, and miniature size of SWNT-based nanosensors with the flexible fluid handling power of microfluidic “lab on a chip” analytical systems. Methods of integrating the SWNT-based sensor into a microfluidic system are compatible with the delicate nature of the SWNT sensor elements. The sensor devices are capable of continuously and autonomously monitoring and analyzing liquid samples in remote locations, and are applicable to real time water quality monitoring and monitoring of fluids in living systems and environments. The sensor devices and fabrication methods of the invention constitute a platform technology, because the devices can be designed to specifically detect a large number of distinct chemical agents based on the functionalization of the SWNT. The sensors can be combined into a multiplex format that detects desired combinations of chemical agents simultaneously.