<p>Time Domain Reflectometry (TDR) is widely used to estimate soil water content; however, its application in column experiments and multilayer systems is often interpreted without fully accounting for the physical and methodological complexities inherent to such configurations. This study identifies the sources of error that arise when TDR rods intersect multiple dielectric layers or pass laterally through column walls and demonstrates how these effects influence apparent permittivity. Experiments conducted in air/water, water/saturated sand, and column/unsaturated sand systems, together with lateral insertion on column tests using two TDRs with different rod lengths, show that transition zones, column’s wall materials, and layer thickness to permittivity ratios can induce deviations of up to 29% in measured permittivity. Parametric analyses further indicate that the Arithmetic and Refractive Index averaging methods do not represent universal regimes but instead vary with geometry and material contrast. In addition, the results show that reference-based correction approaches, such as Heimovaara’s fixed <i>t</i>₁ method, are sensitive to both temperature and the reference material’s electromagnetic properties. This study highlights the limitations of TDR waveform interpretation in column and multilayer configurations, and provides guidance for a more critical assessment of measurements, rather than relying on a single implicit averaging assumption.</p>