Permittivity sensing based on resonance tracking lays the fundamental principle for a variety of biochemical sensors, which has found vast applications in cancer biomarker detection, antigen-antibody analysis, and so on. Driven by continuous promotion of the detection limit, precise environmental control highlights its critical importance. Here, the impacts of liquid level on microwave resonance sensing are investigated, in which a flexible polydimethylsiloxane microfluidic channel and soft tubing are employed to control the liquid under test. The hydraulic pressure affects the effective permittivity of the liquid and the channel material, hence causing extra resonance shift signals. Both contactless and contacting sensing scenarios are studied in numerical simulations and experiments. It is demonstrated that the resonance frequency varies sensitively with the liquid level, and a sensitivity of 343 kHz mm −1 is measured. Meanwhile, a spoof localized surface plasmon resonator and its optimized excitation structure are employed and analyzed for a good figure of merit, addressing the detectability difficulties for high-permittivity and high-loss aqueous solutions. These results provide general guidelines for understanding and controlling the resonance sensors in aqueous environments and help to realize further lower detection limits.