In this study we developed N,N′-dioctyl-3,4,9,10- perylenedicarboximide (PTCDI-C8)-based organic thin film transistors (OTFTs) for sensing applications in aqueous media. We converted an n-channel PTCDI-C8 into a stable device when a fluoropolymer (CYTOP) was positioned between the dielectric and the active layer. The resulting device was stable for up to 2000 h; its electron mobility (μ) improved to 0.29 ± 0.04 cm 2 V -1 s -1 from 0.005 cm 2 V -1 s -1 for the device lacking CYTOP, with the on/off ratio (I on/I off) enhanced by one order of magnitude (from 10 3 to 10 4). By monitoring the shifts in drain current (I DS) and threshold voltage (V th), we used these OTFTs as sensors for different concentrations of potassium phosphate buffer and mercuric(ii) acetate solutions at neutral pH. We also used them to investigated the influence of charge on the detection of insulin at pH 4.5 (where insulin possesses a net positive charge) and pH 7.5 (net negative charge).