The upsurge in the development of RPAS technology for low altitude remote sensing and miniaturized sensors for enhanced imaging, have led to an increase in marine ecological applications. However, the ubiquity of RPAS with sensors in the visible electromagnetic spectrum may be limiting the applications of fine-scale mapping, monitoring, and identification of biogenic marine habitats along temperate intertidal rocky reefs. Here we used a low-cost RPAS coupled with a multispectral sensor (MicaSense® RedEdge™) and object-based image analysis (OBIA) workflow to produce very high-resolution maps of biogenic oyster reefs in Waitemata Harbour, Auckland, New Zealand. The results show that having spectral bands beyond the visible electromagnetic spectrum gradually enhances feature detection on the imagery and increases the potential to delineate targeted features within a heterogeneous marine ecosystem. Using a rule-based classification technique to extract target features, based on their spectral characteristics following segmentation, yielded an overall accuracy of 83.9% and a kappa coefficient of 69.8%.Spectral resolution improved for habitat mapping of oyster reefs with additional spectral bands. High-spatial scale monitoring and mapping of turbid exposed intertidal rocky reefs presents unique challenges, but these challenges can be mitigated by targeting flights during ideal meteorological and oceanographic conditions with RPAS.