Year-long time series of water level are analyzed at five locations along the St. Johns River Estuary, Florida, to investigate propagation of subtidal pulses. Hilbert-transformed Empirical Orthogonal Functions (HEOFs) are obtained after a dominant seasonal signal is extracted from the data. These functions provide information on spatial structure and propagation phase of subtidal water level pulses. The first HEOF mode explains 96% of the subtidal variability and features an unusual spatial structure: amplitude attenuation (averaging 1 mm/km) to 55 km upstream, slight amplification (0.16 mm/km) over the middle 70 km, and attenuation (2.3 mm/km) over the final 18 km of the estuary. The phase suggests a shift from progressive to quasistanding wave behavior at 55 km from the estuary mouth. Additionally, local minima in the phase suggest two sources of subtidal forcing: the coastal ocean and the upstream end. An analytical model describing the evolution of long waves through a channel with frictional damping is fit to the amplitude of HEOF mode 1. Solutions are obtained as a function of two parameters: the nondimensional length of the basin, j, and the nondimensional frictional depth, d. Values of j between 0.55 and 0.67 and d between 1.45 and 1.7 provide the best fit with the HEOF results (1% error or less). These values indicate a highly frictional environment in which the average subtidal wavelength is 10 times the basin length. Subtidal pulses in this estuary, therefore, behave as damped waves that can be represented with idealized models.