Ocean soundscapes are the combination of sounds present at specific times and locations from multiple types of sources, that convey information about habitats and inhabitants in marine ecosystems. Soundscape analysis has the potential to be used in monitoring threatened ecosystems, to timely develop evidence-based conservation and restoration actions. Standardization and validation of data collection and analysis are necessary to ensure the ecological relevance of these methods. Here, we present a series of studies conducted at two Australian World Heritage Sites, the Ningaloo Coast and the Great Barrier Reef, directed at testing and optimizing data collection and analyses. Our research supports that location and position of recorders play an important role in the detected soundscape. We have also observed that the most common ecoacoustic indices used to characterise soundscapes could be skewed by the algorithm parameters used to transform the input pressure waveform. The soundscapes from two different types of healthy and closely located coral reefs can be effectively differentiated using the recently developed Soundscape Code. Our study supports efforts towards the cataloguing of underwater sounds and their association with biological species. These results contribute to standardization and optimization of soundscape analysis as a tool for monitoring and managing coastal habitats.