Tidal waves traveling into estuaries are modified by channel geometry and river flow. The damping effect of river flow on incident astronomical tides is well documented, whereas its impact on low‐frequency tides like MSf and Mm is poorly understood. In this contribution, we employ a numerical model to explore low‐frequency tidal behavior under varying river flow. MSf and Mm are locally generated by frictional mechanisms inside an estuary, and they are larger in amplitude far upstream in tidal rivers and persist landward of the point of tidal extinction. Increasing river flow nonlinearly modulates the longitudinal variations of MSf and Mm amplitudes. This is dynamically explained by flow‐enhanced asymmetry in subtidal friction over the spring‐neap (MSf) and perigee‐apogee (Mm) cycles, respectively. Estuaries act as frequency filters, where low‐frequency waves decay at a smaller rate and propagate more inland than high‐frequency waves. Strong inland penetration of low‐frequency tides informs compound flood management.