The Great Barrier Reef (GBR) of Australia is the largest size of coral reef system on the planet stretching over 2300 kilometers. Coral reefs are experiencing a range of stresses including climate change, which has resulted in episodes of coral bleaching and ocean acidification where increased levels of carbon dioxide from the burning of fossil fuels are reducing the calcification mechanism of corals. In this article, we present a successful application of big data analytics with Internet of Things (IoT)/wireless sensor networks (WSNs) technology to monitor complex marine environments of the GBR. The paper presents a two-tiered IoT/WSN network architecture used to monitor the GBR and the role of artificial intelligence (AI) algorithms with big data analytics to detect events of interest. The case study presents the deployment of a WSN at Heron Island in the southern GBR in 2009. It is shown that we are able to detect Cyclone Hamish patterns as an anomaly using the sensor time series of temperature, pressure and humidity data. The article also gives a perspective of AI algorithms from the viewpoint to monitor, manage and understand complex marine ecosystems. The knowledge obtained from the large-scale implementation of IoT with big data analytics will continue to act as a feedback mechanism for managing a complex system of systems (SoS) in our marine ecosystem.