When time domain reflectometry (TDR) is applied to the field characterization of soil moisture, the waveforms have typically been analyzed using traveltime along the waveguide. The apparent dielectric constant traditionally determined by the traveltime analysis using a tangent-line method does not have a clear physical meaning and is influenced by several system and material parameters. The frequency domain analysis, however, can determine the actual frequency-dependent dielectric permittivity and can be performed using a very short probe. This study presents a numerical modeling approach for common unmatched TDR probes to analyze the TDR signals in the frequency domain. This approach is also adopted to examine how dielectric relaxation, and electrical conductivity affect traveltime analysis. Simulation results indicated that, although the effects of TDR bandwidth and probe length could be quantified and calibrated, the calibration equation for soil moisture measurements was still affected by dielectric relaxation and electrical conductivity, due to differences in soil texture and density. The effects of density can be removed by adding a density term to the calibration equation. Correlating with water content the dielectric permittivity at frequencies between 500 MHz and 1 GHz, rather than the apparent dielectric constant, can minimize the influence of soil texture.