The difference in intensity fluctuation between a surface signal and a submerged signal can be used to discriminate the source depth in the shallow water waveguide. However, the properties of fluctuation distinction in intensity between surface source and submerge source are rarely studied, resulting in the poor performance of fluctuation-based methods sometimes. In this work, the intensity fluctuations caused by source depth fluctuations is analyzed by differential method and variance statistics method to figure out the physics of intensity fluctuations, and to present the suitable quantity for depth discrimination. Firstly, the derivative expression of real part, power and amplitude of the pressure field are respectively derived from the normal mode theory, hence their fluctuation quantities are specified. Then, the numerical examples, including the factor of receiver depth, source frequency and source range, are treated to verify the derivation and summarize the characteristic of fluctuations. The property of the intensity fluctuations is also compared with the distribution of normalized quantity on the depth dimension. Finally, the SWellEx-96 experimental data processing results validate the conclusions. The processing results of derivation, simulation data and experimental data show that the interactions between modes excited by the source give rise to the fluctuations. Meanwhile, the property of the interactions is affected by the received depth, source range and source frequency. Amplitude is capable of building a quantity based on fluctuations for source depth discrimination. For surface and submerged sources with lower frequency, their distinction in their fluctuations is stably represented by amplitude. In the SWellEx-96 experiment, the normalized values calculated from the amplitude of surface noise and submerged sound sources show the lowest difference of 0.5 and the highest difference of 2.5, indicating the effectiveness of using amplitude fluctuations to discriminate the sound source depth.