Coral predation by Crown-of-Thorns Seastars (CoTS) is a major contributor to the coral reef crises in the Indo-Pacific Region, with the 5th wave of outbreaks on the Great Barrier Reef (GBR) since the 1960s likely commencing. Ecology of CoTS larvae is only understood based on aquarium experiments, with limited field observations existing. Based on CoTS specific genetic markers and digital droplet PCR we developed a method to quantify CoTS larvae from plankton samples. We obtained over 7000 plankton samples over the last eight years for monitoring and predicting CoTS outbreaks. Samples obtained were also analysed to obtain details about spawning time of CoTS and weather this varies along the latitudinal gradient of the GBR. Because water quality measurements are available for a subset of samples, we are able to describe the biophysical environment of CoTS larvae. This is important to understand the relationship between CoTS larvae and water quality in the context of the ‘nutrient hypothesis of outbreaks’. We also collected samples from discrete depth using a plankton pump. This data elucidates depth distribution of the larvae and if larvae can exploit sources of nutrition often concentrated in deeper water layers on the GBR shelf.