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This note introduces the estimation of aquifer diffusivity (D) through simultaneous inversion of the attenuation and lag of multiple head fluctuation frequencies due to a dynamic source or boundary, i.e., a river. Spectral analysis, with optimized moving time window length and step size, was used to extract the dominant constituents and their attenuation through space; the cross-power spectral density method was used to determine time lags. The Jacob-Ferris analytical model was then used for inverting for D. Unlike most similar applications to date, here we propose using all frequencies with robust signal-to-noise ratios (five total in our test cases) and both the amplitude attenuation and time lag in the inversion. The method was implemented using observations from wells in the banks of the fluctuating Meghna River in Bangladesh that is connected with a semi-confined sandy alluvial aquifer. The estimated D using the technique provides estimates that are very similar to those from pumping tests. The estimates are more accurate compared to previous implementation of the Jacob-Ferris model on the same data that used only a dominant frequency’s amplitude attenuation or time lag. The workflow and codes for the analysis are provided for straightforward implementation of the robust and cost-effective method.