Pulsed turbidity events caused by factors such as flooding rivers have the potential to seriously impact seagrass communities by depriving the plants of all available light. The effects of light deprivation was investigated on the survival, morphology and physiology of the tropical seagrasses Halodule pinifolia and Halophila ovalis growing in the South-East Gulf of Carpentaria, Australia, a region where pulsed flood events are common. Additionally, physiological and morphological responses to light availability along natural gradients were examined. Responses to both experimental and natural light gradients were investigated for their potential use as indicators of impending seagrass loss during pulsed turbidity events. H. pinifolia was deprived of light for 80 days using in situ shade screens and the following parameters measured at three depths and under the shade screens: biomass, shoot density, canopy height, amino acid content, chlorophyll content, δ 13C signature, %C and sugar concentration. The quantity of light was extremely variable, with mean daily irradiances between 9–12 mol photons m −2 day −1, and a range of 0.05–42 mol photons m −2 day −1. H. pinifolia leaf amino acid content increased with increased water depth (from 8 to 18 μmol g fresh wt.), chlorophyll a to b ratio decreased (from 2.4 to 2.1) and δ 13C values became more negative (from −9 to −12). H. ovalis displayed little tolerance to light deprivation, with plant death occurring after 38 days in the dark. H. pinifolia showed a high degree of tolerance to light deprivation with no biomass loss before day 38 and complete die-off predicted after 100 days. Shoot density, biomass and canopy height all declined after 38 days. Physiological parameters that responded significantly to the light deprivation were the amino acids which increased (from 20 to 80 μmol g fresh wt.), the chlorophyll a to b ratio which decreased (from 2.5 to 2.1) and the values which became more negative (from −9 to −10). Changes in leaf physiology (e.g. amino acid content, chlorophyll content and δ 13C) occurred before morphological changes (e.g. biomass, shoot density, canopy height) or die-off, and were thus considered to be potential indicators of impending seagrass die-off during light deprivation. In conclusion, only long duration (>38 days) pulsed turbidity events would have a detrimental impact on H. pinifolia growing in the Gulf of Carpentaria and that by assessing specific physiological responses, seagrass loss during pulsed turbidity events can predicted.