Low-voltage organic thin-film transistors were fabricated to investigate the stability of organic semiconductors in water and determine the critical parameters for aqueous phase chemical detection. We showed that the molecular structure, alkyl-chain length, and thin-film morphology strongly influence the electrical characteristics in water. Highly two-dimensional films of alkyl-substiruted semiconductors greatly reduced the influence of water on the electrical characteristics. The sensitivity and response times of OTFT sensors were also impacted by the thin-film structure of the organic semiconductor. OTFT sensors were used to detect 10 parts per billion cysteine and 40 ppm TNT in aqueous solutions.