Annual changes in structural attributes and seasonal dynamics in water content, photosynthetic rate and light-use efficiency (LUE) were assessed by spectral transmittance for 4 years (1999-2003) in six stands of a Mediterranean holm oak forest. Green biomass, total biomass and leaf area index (LAI) were determined. In 1999, seasonal dynamics of net carbon dioxide (CO2) exchange and water content were measured. We recorded photosynthetically active radiation (PAR) transmittance and hyperspectral transmittance in the 400-1100 nm region and derived reflectance-based vegetation indices. Transmittance over the PAR region derived from either ceptometer or spectroradiometer measurements (PART and TPAR, respectively) was related to green and total biomass. Both PART and TPAR were also related to LAI (r=0.79 and r=0.70, respectively, P <0.001) and were appropriate for comparison among stands, whereas subtle changes in LAI within a stand were better assessed by the transmittance amplitude in the red edge region (TRE) (within a stand, r=0.77-0.99, P <0.001). Spectral transmittance-based indices successfully captured physiological processes that occurred on temporal (seasonal) and spatial scales. The transmittance-based water index (TWI) was related to both foliage and canopy water content (r=0.69, P <0.001). Estimates of foliage and canopy water content improved in dense (closed) stands (r=0.84 and r=0.87, respectively, P <0.001) compared with low-density stands. Under non-drought conditions, transmittance-based photochemical reflectance index (TPRI) was related to LUE (r=0.58, P <0.05) and net CO2 exchange (r=0.72, P <0.01), and the combined TPAR x TPRI index greatly improved these relationships (r=0.93 and r=0.84, respectively, P <0.01), indicating that both structural and physiological adjustments modified CO2 fixation capacity in these forest stands. Our novel approach to the study of transmitted radiation provides a tool for estimating structural and functional variables such as LAI, LUE and water content, which are key determinants of terrestrial productivity.