The interactions of guided acoustic waves with pipelines and associated components has become a topic of interest due to their application in water pipeline condition assessment. In this paper, guided acoustic wave interactions with flanged junctions in a water-filled pipeline are investigated by an analytical model and experimental measurements. In the model, axial wavenumbers, displacement, and stress profiles of the main pipeline and flange junction components are calculated by an existing cylindrical waveguide analytical model. These components are then concatenated together using mode matching to determine the overall theoretical characteristics. Experiments with a flanged water-filled steel pipeline are carried out to verify model predictions. Transmitted signals are acquired using acoustic transducers uniformly spaced along the pipeline axis to separate individual modes and extract mode amplitudes. Transmission losses are estimated by comparing the extracted amplitudes in a pipeline with and without the flanged junction. Both theoretical predictions and experimental results indicate that the flanged junction interacts with pipeline wall dominant modes by transforming them into waterborne modes and as a result guides acoustic power into the water medium. The flange is shown to cause a small transmission loss in waterborne modes as compared to the pipeline without flanges.