Marine habitats are subject to monitoring activities to assess the impact of climate change, as required by EU and national directives. Coralligenous reefs are typical Mediterranean underwater seascapes, which originate from the growth of calcareous bioconstructions, including <em>Lithophyllum stictiforme</em>, a slow-growing calcareous red algae. The impact of temperature variations on its growth has only recently been investigated in the field, although with destructive sampling methods. The MANATEE (Monitoring and mApping of mariNe hAbitat with inTegrated gEomatics technologiEs) project aims to establish a non-destructive monitoring approach by leveraging geomatic techniques and underwater photogrammetry. The project will test three optical-based systems for divers and on different types of uncrewed underwater vehicles – UUVs (a low-cost micro Remotely Operated Vehicle – ROV and an observation-class UUV). This article presents the experimental procedure to verify that the developed underwater photogrammetry-based method can guarantee the detection of millimetre-level changes per year in the algae growth. A statistically significant number of samples were collected, prepared, and fixed on specially designed tiles and nets featuring photogrammetric targets and placed on the seabed. Following metric traceability principles, control elements (calibrated scale bars and colour checkers) were employed to verify geometric and colorimetric results of underwater photogrammetric surveys. The focus here is on the geometric verification, and the analyses presented demonstrate how the sub-millimetre accuracy potential and reproducibility meet the requirements for <em>Lithophyllum stictiforme</em> monitoring.