We report simple and effective methods to develop long-term, stable silicon nanowire-based pH sensors and systematic studies of the performance of the developed sensors. In this work, we fabricate silicon nanowire pH sensors based on top-down fabrication processes such as E-beam lithography and conventional photolithography. In order to improve the stability of the sensor performance, the sensors are coated with a passivation layer (silicon nitride) for effective electrical insulation and ion-blocking. The stability, the pH sensitivity, and the repeatability of the sensor response are critically analyzed with regard to the physics of sensing interface between sample liquid and the sensing surface. The studies verify that the sensor with a passivation layer over critical thickness show long-term, stable sensor response without long-term drift. The studies also show the detection of pH level with silicon nanowire sensors is repeatable only after proper rinsing of sensor surfaces and there exists trade-off between the stability and the pH sensitivity of sensor response.