A simple, highly sensitive square-wave voltammetric method is reported for the sensing of paraquat (PQ) in natural water samples. A glassy carbon electrode modified with functionalized multiwalled carbon nanotubes (MWCNTs) immobilized within a Dihexadecylhydrogenphosphate (DHP) film was prepared and characterized with cyclic, differential-pulse and square-wave voltammetry. The modified electrode was found to exhibit a remarkably enhanced electro-activity toward the sensing of paraquat. Under optimum experimental conditions, using square wave voltammetry, the sensing of paraquat is achievable over the concentration range from 5.0×10−8 to 1.5×10−6molL−1 with a detection limit (3σ) of 1.0×10−8molL−1. The protocol is explored toward potential interferents and is applied for the analysis of paraquat in natural waters with the results agreeing with independently verified HPLC at a 95% confidence level.