The influence of water column variability on low-frequency, shallow water geoacoustic inversion results is considered. The data are estimates of modal eigenvalues obtained from measurements of a point source acoustic field using a horizontal aperture array in the water column. The inversion algorithm is based on perturbations to a background waveguide model with seabed properties consistent with the measured eigenvalues. Water column properties in the background model are assumed to be known, as would be obtained from conductivity, temperature, and depth measurements. The scope of this work in addressing the impact of water column variability on inversion is twofold. Range-dependent propagation effects as they pertain to eigenvalue estimation are first considered. It is shown that mode coupling is important even for weak internal waves and can enhance modal eigenvalue estimates. Second, the effect of the choice of background sound speed profile in the water column is considered for its impact on the estimated bottom acoustic properties. It is shown that a range-averaged sound velocity profile yields the best geoacoustic parameter estimates.