The quantum yield of photosystem II (φII, also termed ΔF/Fm' or Fv/Fm in light- or dark- acclimated plants, respectively) of the tropical seagrass Halophila stipulacea was measured in situ using modulated fluorescence techniques over diel periods at a range of depths. Photosynthetic elec- tron transport rates (ETRs), as derived from φII values at specific ambient photosynthetically available radiation (PAR) irradiances, increased in direct proportion to increasing irradiance in the morning and, at shallow sites (7 to 10 m), reached saturating rates and then declined in the afternoon with lower PAR-specific ETRs. On the other hand, plants at 32 to 33 m showed no saturation even at mid- day, and the percentage reduction in PAR-specific afternoon ETRs was less than that of the shallower plants. The use of an automated shutter in the measuring device enabled non-photochemical quenching due to down-regulation and basal intrinsic non-radiative decay to be distinguished. While midday values of down-regulation were lower in deeper water, basal intrinsic non-radioactive decay remained fairly constant at 30 to 40% at all depths, with more variation in shallow waters. The maxi- mal φII (i.e. Fv/Fm) reached similar values at midnight regardless of depth. H. stipulacea acclimates to the widely varying irradiances across this depth gradient by regularly modulating down-regulation- based non-photochemical quenching processes, while dissipating a large proportion of light energy through intrinsic decay regardless of depth.