The dynamics of large isolated sand dunes moving across a gravel lag layer were studied in a supply-limited reach of the River Rhine, Germany. Bed sediments, dune geometry, bedform migration rates and the internal structure of dunes are considered in this paper. Hydrodynamic and sediment transport data are considered in a companion paper. The pebbles and cobbles (D50 of 10 mm) of the flat lag layer are rarely entrained. Dunes consist of well-sorted medium to coarse sand (D50 of 0·9 mm). Small pebbles move over the dunes by ‘overpassing’, but there is a degree of size and shape selectivity. Populations of ripples in sand (D50 < 0·6 mm), and small and large dunes are separated by distinct breaks in the bedform length data in the regions of 0·7–1 m and 5–10 m. Ripples and small dunes may have sinuous crestlines but primarily exhibit two-dimensional planforms. In contrast, large dunes are primarily three-dimensional barchanoid forms. Ripples on the backs of small dunes rarely develop to maximum steepness. Small dunes may achieve an equilibrium geometry, either on the gravel bed or as secondary dunes within the boundary layer on the stoss side of large dunes. Secondary dunes frequently develop a humpback profile as they migrate across the upper stoss slope of large dunes, diminishing in height but increasing in length as they traverse the crestal region. However, secondary dunes more than 5 m in length are rare. The dearth of equilibrium ripples and long secondary dunes is probably related to the limited excursion length available for bedform development on the parent bedforms. Large dunes with lengths between 20 m and 100 m do not approach an equilibrium geometry. A depth limitation rather than a sediment supply limitation is the primary control on dune height; dunes rarely exceed 1 m high in water depths of ≈4 m. Dune celerity increases as a function of the mean flow velocity squared, but this general relationship obscures more subtle morphodynamics. During rising river stage, dunes tend to grow in height owing to crestal accumulation, which slows downstream progression and steepens the dune form. During steady or falling stage, an extended crestal platform develops in association with a rapid downstream migration of the lee side and a reduction in dune height. These diminishing dunes actually increase in unit volume by a process of increased leeside accumulation fed by secondary dunes moving past a stalled stoss toe. A six-stage model of dune growth and diminution is proposed to explain variations in observed morphology. The model demonstrates how the development of an internal boundary layer and the interaction of the water surface with the crests of these bedload-dominated dunes can result in dunes characterized by gentle lee sides with weak flow separation. This finding is significant, as other studies of dunes in large rivers have attributed this morphological response to a predominance of suspended load transport.