Underwater sound propagation in a rapidly evolving shallow-water ocean has high temporal and spatial variability. To ensure the performance of acoustic inversion techniques to locate a sound source or estimate the sea-bottom parameters, it is necessary to take into account the water column variability, which can be done by introducing the empirical orthogonal functions (EOFs), which describe the water column variability, into the environmental model used for the inversions. However, in a range-dependent and time varying ocean, one needs to regularly update the EOFs according to the scales of environmental, spatial, and temporal coherence, or the EOFs may not be the most efficient and optimal vector bases to decompose the dynamic ocean field. In this paper, the environmental data collected during the New Jersey Shallow Water 2006 (SW06) experiment are analyzed to check the environmental coherence scales in the experimental site. The analysis results provide a guideline as to when and where one should update the EOF bases. The observation of the SW06 acoustic signal coherence is reported and correlated to the environmental variability. Finally, acoustic inversions using the SW06 data are performed, and the effects of using insufficient water-column EOFs are investigated.