Photosynthetic activity of three seagrass species, Posidonia sinuosa Cambridge et Kuo, Posidonia australis Hook. f. and Halophila ovalis (R. Br.) Hook., growing in Cockburn Sound, Western Australia, was assessed using an underwater pulse amplitude modulated fluorometer (Diving-PAM). The study aimed to determine possible causes and the extent of stress to seagrasses during transplantation, so that rehabilitation efforts can be improved by reducing stress during the transplant process. Absorptance factors for each species were determined as 0.64 ± 0.04 for P. sinuosa, 0.59 ± 0.02 for P. australis and 0.55 ± 0.02 for H. ovalis, which were substantially lower than previously reported photosynthetic absorption factors. Transmittance, reflectance and non-photosynthetic absorptance of light diverted between 35-45% of irradiance from use in photosynthesis. An investigation of potential errors during measurement of rapid light curves (RLCs) reinforced the importance of ensuring that leaves remained stationary in the Universal Sample Holder. Any movement of seagrass leaves resulted in incorrect measurements of electron transport rates (ETR). A study on seasonal photosynthetic rates of each species found that maximum ETR (ETRmax) varied seasonally and among species. The highest ETRmax for each species occurred during summer, when ambient irradiances were at a maximum, and decreased during autumn. H. ovalis had the highest overall ETRmax in summer, followed by P. australis and P. sinuosa. Effective quantum yield(ΔF/Fm′)of each species varied seasonally, changing inversely with irradiance, which agrees with previously reported studies. ETRmax for each species also showed a diurnal pattern coincident with irradiance throughout the day. The ÄF/Fm for all species demonstrated a diurnal decrease in photosynthetic efficiency coincident with the midday irradiance maximum. Large natural variation in ETR was detected in all species, indicating that the effects of external stress on ETR may be difficult to detect. Two adjacent, physically separated seagrass meadows were examined to determine if apparent visual differences between the sites were reflected by measured physical and photosynthetic characteristics. ETR, leaf area index and sediment grain size differed between sites, but ΔF/Fm, canopy height, shoot density and epiphyte biomass did not, indicating a poor connection between physical and photosynthetic characteristics at these two meadows. Therefore caution should be used when attempting to visually assess the photosynthetic activity of a site based on physical characteristics. Changes in photosynthetic activity were monitored to determine seagrass stress during transplantation, and post-transplantation recovery. Two transplantation methods, sprigs and plugs, were examined, and photosynthetic activity was compared before, during and after transplantation. ETRmax of sprigs took one to two months to increase to the same level recorded at a control meadow, primarily due to desiccation stress suffered during transport. The ΔF/Fm′ decreased below 0.2 after transplantation, but fully recovered after three months. Survival of sprigs was reduced due to strong currents and heavy epiphytic fouling. The ETRmax of transplanted plugs (5, 10 and 15 cm diameter) took up to one week to recover to the same level recorded at a control meadow. Survival of plugs was reduced due to winter swells and storms. Since the leading human-controlled cause of transplant failure was desiccation stress, future transplanting efforts should endeavour to keep seagrasses submerged at all times during the transplanting process.