The variability in land surface heat (H), water vapor (LE), and CO2 (or net ecosystem exchange, NEE) fluxes was investigated at scales ranging from fractions of seconds to years using eddy-covariance flux measurements above a pine forest. Because these fluxes significantly vary at all these time scales and because large gaps in the record are unavoidable in such experiments, standard Fourier expansion methods for computing the spectral and cospectral statistical properties were not possible. Instead, orthonormal wavelet transformations are proposed and used. The are ideal at resolving process variability with respect to both scale and time and are able to isolate and remove the effects of missing data (or gaps) from spectral and cospectral calculations. Using the spectra, we demonstrated unique aspects in three appropriate ranges of time scales: turbulent time scales (fractions of seconds to minutes), meteorological time scales (hour to weeks), and seasonal to interannual time scales corresponding to climate and vegetation dynamics. We have shown that: (1) existing turbulence theories describe the short time scales well, (2) coupled physiological and transport models (e.g. CANVEG) reproduce the wavelet spectral characteristics of all three land surface fluxes for meteorological time scales, and (3) seasonal dynamics in vegetation physiology and structure inject strong correlations between land surface fluxes and forcing variables at monthly to seasonal time scales. The broad implications of this study center on the possibility of developing low-dimensional models of land surface water, energy, and carbon exchange. If the bulk of the flux variability is dominated by a narrow band or bands of modes, and these modes “resonate” with key state and forcing variables, then low-dimensional models may relate these forcing and state variables to NEE and LE.