This paper investigates the influence of water column variability on the estimates of geoacoustic model parameters obtained from matched field inversions. The acoustic data were collected on the New Jersey continental shelf during the Shallow Water 2006 experiments. The oceanographic variability was evident when the data were recorded. To quantify the uncertainties of the geoacoustic parameter estimates in this environment, Bayesian matched field geoacoustic inversion was applied to multi-tonal continuous wave data. The spatially and temporally varying water column sound speed was parametrized in terms of empirical orthogonal functions and included in the inversion. Its impact on the geometric and geoacoustic parameter estimates was then analyzed by the inter-parameter correlations. Two different approaches were used to obtain information about the variation of the water sound speed. One used only the profiles collected along the experimental track during the experiment, and the other also included observations from a larger area and a greater time period. The geoacoustic estimates from both the large and small sample sets were consistent. However, due to the diversity of the oceanic sound speed, more empirical orthogonal functions were needed in the inversion when more sound speed provile samples were used.

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