The detection of biomarkers in the liquid phase using mechanical sensors is difficult because of noise caused by the liquid. To reduce and verify the side effects of liquid loading, we performed calculations and experiments to determine the shift in resonant frequency according to the loading conditions. A 2-μm-thick piezoelectric rectangular micro-diaphragm with a 500 × 500 μm membrane was used. These dimensions were determined such that there would be an analogous resonant frequency shift ratio in both (1, 1) and (2, 2) modes. By calculating and measuring the resonant frequency, we verified that the resonant frequency of the sensor would change only through contact with the liquid, even the resonant frequency change by only liquid much higher than the changes caused by the nanoparticles. The real signal constituted only 0.017% of the initial resonant frequency. To enhance the sensitivity by reducing the unexpected surface stress in the liquid, the liquid was dropped onto the surface of the micro-diaphragm. This resulted in an improvement of more than 10 times the sensitivity in both modes. In addition, by controlling the position in the micro-diaphragm resonating sensor, more sensitive positions with large displacements were determined according to each mode.