Soil salinity has a major impact on agricultural production. In a changing climate with rising sea-levels, low-lying coastal areas are increasingly inundated whereby saltwater gradually contaminates the soil. Drought prone areas may suffer from salinity due to high evapotranspiration rates in combination with the use of saline irrigation water. Salinity is difficult to monitor because soil moisture affects the soil’s spectral signature. We conducted Fourier-transform infrared spectroscopy on alluvial and sandy soil samples in the coastal estuary of the Red River Delta. The soils are contaminated with NaCl, Na2CO3 and Na2SO4 salts. In an experiment of salt contamination, we established that three ranges of the spectrum were strongly influenced by both salt and moisture content in the soil, at wavenumbers 3200–3400 cm−1 (2.9–3.1 µm); 1600–1700 cm−1 (5.9–6.3 µm); 900–1100 cm−1 (9.1–11.1 µm). The Na2CO3 contaminated soil and the spectral value had a linear relationship between wavelengths 6.9 and 7.4 µm. At wavelength 6.99 µm, there was no relationship between absorbance and soil moisture, but the absorbance was proportional to the salt content (R2 = 0.85; RMSE = 0.68 g) and electrical conductivity (R2 = 0.50; RMSE = 3.8 dS/m). The relationship between soil moisture and spectral absorbance value was high at wavelengths below 6.7 µm, resulting in a quadratic relation between soil moisture and absorbance at wavelength 6.13 µm (R2 = 0.80; RMSE = 5.2%). The spectral signatures and equations might be useful for mapping salt-affected soils, particularly in difficult to access locations. Technological advances in thermal satellite sensors may offer possibilities for monitoring soil salinity.