Geoacoustic inversion using fluctuating signal observations can be challenging. The origin of these fluctuations needs to be understood so the signals can be used appropriately. A set of experiments [Tang et al., Oceanogr. 20(4), 156-167 (2007)] was carried out in shallow water near the New Jersey shelf break in summer 2006. Significant fluctuations in the direct path and surface-reflected arrivals of short-range chirp transmissions (1.1-2.9 kHz) were observed on a vertical line array. This paper explains the origin of these signal fluctuations through analysis of the arrival amplitudes. It is shown that the strong thermocline combined with an oscillating source motion due to ocean surface waves results in the signal fluctuations.