The balise transmission system (BTS) is essential for train position sensing and safe operation. Transmission loss is a key parameter particularly required for the evaluation of systems. The eddy current loss (ECL), caused by the conductivity of debris, affects the transmission performance of the BTS when the balise is immersed in water. This study proposes an effective modeling for the BTS using S-parameters. Utilizing the electromagnetic coupling analysis in the near-field region, we derived an equivalent circuit with the frequency and conductivity of water taken into consideration. The S21 can be predicted accurately by using the proposed equivalent circuit. For validation, a BTS system was implemented and measured to compare with theoretically calculated results and electromagnetic simulation results in the main lobe zone. The measurement results, simulation, and calculation were in good agreement. Moreover, the modeling was used to predict the I/O characteristics of the balise. The power of the balise uplink FSK signal was measured in the water debris and found to be approximately 0.62 dB less than in air. These findings aligned well with theoretical predictions.