Excretion experiments were conducted at the Lizard Island Research Station on the Great Barrier Reef with the common holothurians Stichopus chloronotus and Holothuria atra, during January 1996 (summer) and June 1997 (winter). Specimens were collected from depths between 1 and 9 m.Experiments were performed in acid-washed jars containing filtered seawater, which were closed with plastic lids fitted with a tube for aeration and a tube for water sampling. Animals were deprived of sediment for a least 48 hours before being transferred to incubation jars and left to adapt for 10 minutes before initial water samples were taken. After 180-240 minutes (depending on the size of the animal) final water samples were taken and the wet weight of each individual measured. For each parameter measured, duplicate 10 ml samples were filtered, immediately frozen (-20°C) and later transported to AIMS for analyses. Samples from minimum of 24 individuals of each species were analysed per season. In June 1997, excretion rates of 9 anterior and 9 posterior sections of both species, resulting from asexual reproduction by fission, were measured. Also, two time-series experiments, each with 3 individuals and a control were performed to validate the assumption of constant excretion rates. Water samples were taken at 0 (before) and 5, 15, 30, 60, 90, 120 and 180 min after addition of animals. All summer water samples were analysed for ammonium and phosphate. DOP and DON, nitrate and nitrite were only analysed for a subset of samples. All winter samples were analysed for ammonium and phosphate. DOP and DON, nitrate and nitrite were only analysed for the time-series samples.Ammonium concentrations in water expelled during respiration in 20 individuals of each species were measured by quickly removing the animals from the holding tank and ejecting water (5 ml) from the anus. Concentrations were compared with ambient water in the holding tank. On the reef flat at Great Palm Island, water directly (~2 cm) behind 15 individuals of each species and 15 controls were sampled.The linear distance travelled by single animals was used to estimate the sediment area in direct contact with holothurians. In each of four experiments, 20-23 individuals were tagged and the start marked. After 60-120 minutes, the distance travelled was measured and converted to hourly rates, which were multiplied by the average breadth of the ventral surface of the holothurian. To estimate the area of sediment microflora which might be directly affected by excretion, a tank was set up with fine sediment (<0.125 µm) covering a white floor. For each Stichopus chloronotus individual, the area of sand displaced behind the animal by each expiration was calculated for 10 expirations and the frequency of expiration recorded.