Coastal ecosystems are under threat by an increasing number of natural and anthropogenic stressors. These stressors co-occur in countless combinations, raising questions in the scientific community about their combined and/or interactive effects on individuals, populations and ecosystems. Environmental management of multiple stressors is challenging, as the governance of stressors are still largely based on individual effects, despite growing evidence of interactive effects in coastal ecosystems. As a result, the field of multiple stressor research is rapidly expanding to better understand, predict and manage stressor interactions. This thesis aims to address questions surrounding deteriorating water quality, as an indication of ecosystem health, of the Great Barrier Reef (GBR). Land-based runoff has been identified as the greatest contributor to poor water quality in inshore marine ecosystems, such as the GBR. The three main water quality pollutants common to the GBR include pesticides, excess nutrients and suspended sediments. These pollutants originate from coastal development and agricultural practices and are transported to receiving waters via flood plumes. Following high rainfall during the Queensland wet season, GBR ecosystems are simultaneously exposed to high concentrations of pesticides, nutrients and sediments. This thesis presents a collection of related chapters that assess the effects of these three water quality stressors on coastal ecosystems.