Underwater soundscapes are increasingly applied in ecosystem monitoring and biodiversity assessment. This chapter synthesizes ecoacoustic research conducted across two World Heritage areas (the Great Barrier Reef and the Ningaloo Coast) encompassing multiple coastal habitats, including coral reefs, macroalgal meadows, and sand flats. We demonstrate that soundscape analyses can reliably discriminate among habitats and resolve fine-scale ecological variation within coral reefs. These findings confirm relations between acoustic patterns, habitat structure, and the activity of associated biological communities. However, soundscapes are not only influenced by ecological processes, but also by both physical and computational processes. Experimental assessments show that hydrophone distance and orientation to the target habitat can alter received sound pressure levels due to sensor directivity. Analytical choices (e.g., sampling frequency, Fourier transform parameterization, window overlap) influence acoustic indices outputs and potentially affect comparisons and interpretations. Robust ecological inference from passive acoustic monitoring requires transparent reporting of deployment and analytical parameter choices, and assessment metric sensitivity. Adopting such best-practice frameworks will enhance the reliability, comparability, and long-term utility of ecoacoustics as a tool for coastal ecosystem monitoring and conservation.