The estimation of horizontal wave-number variations in a stochastic shallow-water environment at the Atlantic Generating Station (AGS) site is constructed. A method using empirical orthogonal functions has been developed [Longfritz et al., J. Acoust. Soc. Am. 97, 3316 (A) (1995)] to relate wave-number fluctuations to environmental variations. First, the AGS site is modeled as a stochastic shallow channel with a range-dependent layered sediment bottom. The layer interface depths and intralayer sound speeds are treated as random variables. Then, the estimation procedure is applied to a particular propagation track, where geoacoustic profiles and acoustics measurements are both available. Environmental profiles along the track are treated as a sample from a stochastic ensemble. Estimates are obtained for both the range variance of the wave numbers and the particular deviations associated with each profile in the sample. Comparisons are made between results from the estimation procedure and simulations from the KRAKEN propagation code. In a separate study, acoustical wave numbers have been generated from experimental data for the track using a method of Thomson. The estimation results are compared to this data.