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Sampling water from small-diameter wells using narrow access tubes is a challenging problem in field research efforts. In this study, a simple, easy-to-use embedded inertial pump is used for sampling groundwater from small-diameter wells. Performance of the embedded inertial pumps with different designs was demonstrated at a high-resolution field tracer experiment site near Beijing, China. Tests on the effects of primary pump design variables (stroke frequency, amplitude and diameter of pump tube) and secondary variable (ball valve diameter, the distance between hollow cylinders, and slot depths) were conducted. A linear equation is set up to describe the relationship between flow rate and primary pump design variables. The data show that a motion frequency value of 1–4 Hz and amplitude around 20 cm could satisfy effective groundwater sampling for both manual and automotive operations. The ball valve diameter should be designed to accommodate the delivery tube and hollow cylinders, because it determines the overall effective cross-sectional area; higher sectional area implies higher flow rate. The distance between hollow cylinders is recommended as 1.5–2 times of ball valve diameter. The proposed pump design is a low-cost approach for sampling from multi-channel wells, which are used for conducting three-dimensional tracer tests or groundwater monitoring that requires sampling at high temporal and spatial resolution.