This two-part paper provides comprehensive time and frequency domain analyses and models of along-channel water level variations in the 234-km-long Lower Columbia River and Estuary (LCRE) and documents the response of floodplain wetlands thereto. In Part I, power spectra, continuous wavelet transforms, and harmonic analyses are used to understand the influences of tides, river flow, upwelling and downwelling, and hydropower operations (“power-peaking”) on the water level regime. Estuarine water levels are influenced primarily by astronomical tides and coastal processes and secondarily by river flow. The importance of coastal and tidal influences decreases in the landward direction, and water levels are increasingly controlled by river flow variations at periods from ≤1 day to years. Water level records are only slightly nonstationary near the ocean, but become highly irregular upriver. Although astronomically forced tidal constituents decrease above the estuary, tidal fortnightly and overtide variations increase for 80–200 km landward, both relative to major tidal constituents and in absolute terms. Near the head of the tide at Bonneville Dam, strong diel and weekly fluctuations caused by power-peaking replace tidal daily (diurnal and semidiurnal) and fortnightly variations. Tides account for 60–70 %, river flow and seasonal processes 5–20 %, and weather 2–4 % of the total variance in the seaward 60 km of the system. In the landward 70 km of the LCRE, seasonalfluvial variations account for 80–90% of the variance, powerpeaking 1–6 %, and tides <5 %. In Part II, regression models of water levels and inundation patterns are used to understand the distribution of floodplain wetlands, and a system zonation is defined based on bedrock geology, hydrology, and biota.