We experimentally investigate the flow through a hollow cube, with an indoor ground-level passive scalar source, immersed in a rough-wall turbulent boundary layer inside a water tunnel. The focus is on characterizing scalar transport within the cube, through simultaneous scalar and flow measurements using planar laser-induced fluorescence and particle image velocimetry. To understand the role of window positioning, three cube configurations, labelled as ‘centre’, ‘up-down’ and ‘down-up’, distinguished by window positions at the upstream and downstream ends, are studied. Varying window position alters the flow characteristics within the cube, resulting in differences in scalar concentration and distribution. The steady-state concentration is highest for ‘centre’, followed by ‘up-down’ and ‘down-up’ configurations. Regarding the scalar distribution, ‘centre’ showed accumulation near the top and bottom walls, while ‘up-down’ and ‘down-up’ exhibited scalar buildup in the lower and upper half of the cube, respectively. The flow patterns and scalar transport mechanisms remained consistent across different Reynolds numbers ($Re=U_{Ref}H/\nu = 20\ 000$, 35 000, 50 000) for each configuration; $U_{Ref}=$ incoming flow velocity at cube height ($H$), and $\nu =\,$ kinematic viscosity of water. The analysis is extended by revising the classical box model, accounting for practical complexities such as non-perfect mixing. Our results can help better understand and model indoor–outdoor pollutant exchange in complex urban environments.