Several effects of nearly isotropic free-stream turbulence in transitionally rough turbulent boundary layers are studied using data obtained from laser Doppler anemometry measurements. The free-stream turbulence is generated with the use of an active grid, resulting in free-stream turbulence levels of up to 6.2%. The rough surface is characterized by a roughness parameter k+ ≈ 53, and measurements are performed at Reynolds numbers of up to Reθ = 11300. It is confirmed that the free-stream turbulence significantly alters the mean velocity deficit profiles in the outer region of the boundary layer. Consequently, the previously observed ability of the Zagarola & Smits (J. Fluid Mech., vol. 373, 1998, p. 33) velocity scale U∞δ*/δ to collapse results from both smooth and rough surface boundary layers, no longer applies in this boundary layer subjected to high free-stream turbulence. In inner variables, the wake region is significantly reduced with increasing free-stream turbulence, leading to decreased mean velocity gradient and production of Reynolds stress components. The effects of free-stream turbulence are clearly identifiable and significant augmentation of the streamwise Reynolds stress profiles throughout the entire boundary layer are observed, all the way down to the inner region. In contrast, the Reynolds wall-normal and shear stress profiles increase due to free-stream turbulence only in the outer part of the boundary layer due to the blocking effect of the wall. As a consequence, there is a significant portion of the boundary layer in which the addition of nearly isotropic turbulence in the free-stream, results in significant increases in anisotropy of the turbulence. To quantify which turbulence length scales contribute to this trend, second-order structure functions are examined at various distances from the wall. Results show that the anisotropy created by adding nearly isotropic turbulence in the free-stream resides mostly in the larger scales of the flow. Furthermore, by analysing the streamwise Reynolds stress equation, it can be predicted that it is the wall-normal gradient of 〈u2v〉 term that is responsible for the increase in 〈u2〉 profiles throughout the boundary layer (i.e. an efficient turbulent transport of turbulence away from the wall). Furthermore, a noticeable difference between the triple correlations for smooth and rough surfaces exists in the inner region, but no significant differences are seen due to free-stream turbulence. In addition, the boundary layer parameters δ*/δ95, H and cf are also evaluated from the experimental data. The flow parameters δ*/δ95 and H are found to increase due to roughness, but decrease due to free-stream turbulence, which has significance for flow control, particularly in delaying separation. Increases in cf due to high free-stream turbulence are also observed, associated with increased momentum flux towards the wall.