Great Barrier Reef Australia (GBR) is affected by cold water intrusions originating in the Coral Sea and upwelled on the reef. Therefore biological interest in GBR upwelling has been driven by the view that upwelled waters rich in nutrients boost plankton production and overall productivity of the GBR system. We propose to employ a Sensor Network for in situ monitoring of upwellings. Temperature is a good proxy for upwelling however 3D dense spatial data is required to describe upwelling and their impact on plankton abundance. The array of underwater sensors is deployed at various depth on the coral reef in Nelly Bay, Magnetic Island, GBR.. We propose that the temperature data is communicated real time via ad hoc network using RF signal to the on-shore base station. This permits us to collect the plankton data in real-time synchronized to the temperature changes. This paper outlines the methods of the deployment of sensor networks for ecological research.