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In a time of ever-increasing pressure on the coastal ocean and rising costs, the development of effective and efficient methods for assessing the health of marine ecosystems is becoming essential for continued conservation efforts. Taking advantage of technologies such as remotely operated vehicles (ROVs) may be a way of achieving this, but a quantitative check on the quality of ROV-derived data is necessary. Here, using coralline algae reefs (maerl beds) as a model habitat, we compared 3D seabed reconstructions obtained from structure-from-motion photogrammetry surveys from diver-held and ROV-mounted camera systems. We found that both approaches achieved satisfactory alignment and mm-scale resolution, allowing small-scale features and individual organisms in the maerl bed to be resolved. The higher quality camera system available to divers resulted in generally lower modelling errors, but the spatial extent of surveys was highly restricted. In contrast, although associated with a slightly higher error, we show that much larger areas can be surveys by ROVs—we reconstructed 11,285 m2 of seabed in just 400 min of ROV deployment time. Moving forward, we recommend that a hybrid survey approach is adopted: utilising ROV surveys for large-scale monitoring and diver surveys for higher detail insights that are informative for areas with highly complex and fine-scale morphologies (like coralline algae reefs). Here, even small changes in complexity can be indicative of habitat change, and associated species can be small in size so multiscale visual assessment is beneficial.