An in situ calibration system is a versatile exploration instrument for electrochemical sensors investigating the biochemical properties of the marine environment. The purpose of this paper is to describe the design of an auto-calibrating system for electrochemical (pH) sensors, which permits two-point in situ calibration, suitable for long-term measurement in deep sea aqueous environments. Holding multiple sensors, the instrument is designed to perform long-term measurements and in situ calibrations at abyssal depth (up to 4000 m). The instrument is composed of a compact fluid control system which is pressure-equilibrated and designed for deep-sea operation. In situ calibration capability plays a key role in the quality and reproducibility of the data. This paper focuses on methods for extending the lifetime of the instrument, considering the fluidics design, mechanical design, and low-power consumption of the electronics controller. The instrument can last 46 d under normal operating conditions, fulfilling the need for long-term operation. Data concerning pH measured during the KNOX18RR cruise (Mid-Atlantic Ridge, July-August, 2008) illustrate the desirable properties of the instrument. Combined with different electrodes (pH, H-2, H2S, etc.), it should be of great utility for the study of deep ocean environments, including water column and diffuse-flow hydrothermal fluids.