Tropical port environments represent a growing extent of artificial substrate along the Great Barrier Reef (GBR) coast, yet benthic communities colonising this infrastructure remain poorly characterised. The existing TropWATER and NQBP water quality monitoring programme deploys continuous loggers to record turbidity and multispectral benthic photosynthetically active radiation (PAR), supplemented by sampling trips every 6–8 weeks to collect samples and physiochemical measurements. While current seagrass and coral monitoring programmes assess broad-scale habitat changes, this study evaluates whether the water quality monitoring can be leveraged to characterise the recruitment of specific benthic communities. By deploying standardised recruitment substrates during routine monitoring visits, this research will focus on fine-scale dynamics of recruitment for hard-fouling invertebrates, encrusting and colonial taxa, and invasive species. This study aims to assess whether water quality thresholds associated with shifts in community composition and succession trajectories can be determined by linking continuously monitored parameters to recruitment and succession dynamics, including community responses to discrete disturbance events such as storms, runoff, and dredging operations. Findings will help inform ecological engineering approaches for development in tropical coastal ecosystems, identifying timing and substrate characteristics, and site conditions that maximise biodiversity and minimise risk of invasive species establishment.