We have investigated a diamond crystal that consists of several misorientated subgrains. The main feature of the crystal is the dark areas in the cathodoluminescent core that has ‘estuary-like’ boundaries extending along the subgrain interfaces. The core has >3100 ppm of nitrogen, and the share of the B form is >95%; the absorbance of the centre N3VH at 3107 cm–1 reaches 75 cm–1. The N3 centre absorbance, as well as N3 luminescence, is absent in the core. In the outer part of the crystal, bright blue luminescence of the N3 centre is apparent, and the N3 absorbance reaches 5.3 cm–1. These observations could be explained by the conversion of N3 centres to N3VH after attaching a hydrogen atom. After the full conversion of the N3 centres, the diamond becomes darker under CL. We hypothesise the dark core has a specific shape due to the post-growth diffusion of the hydrogen.