Open channel flows subjected to a longitudinal transition in roughness, from bed friction to emergent cylinder drag and vice versa, are investigated experimentally in an 18 m long laboratory flume. These are compared to uniform flows subject to (1) bed roughness only and (2) an array of emergent vertical cylinders installed on bed roughness. The nearbed region is investigated in detail for uniform flows through the cylinder array. The water column can be divided into two parts: a region of constant velocity and a boundary layer near the channel bed. In the latter region, a local increase in velocity, or velocity bulge, is observed in line of a cylinder row. The velocity bulge may be related to the disorganization of the von Kármán vortex street by the bed-induced turbulence, resulting in reduced momentum loss in the cylinder wake. The boundary layer height is found to be independent of water depth and bed roughness (smooth or rough bottom). Strong oscillations of the free surface (seiching) are observed. Oscillation amplitude is dependent on the longitudinal position within the cylinder array and is found to decrease with decreasing array length. When water depth/boundary layer height ratio is close to unity, the disorganization of the von Kármán vortex street throughout the water column prevents seiching from occurring. In the case of roughness transition flows, the water depth is found to vary only upstream of the change in roughness. Vertical profiles of velocity and turbulence are self-similar upstream of the transition and collapse with the uniform flow profiles. Downstream of the roughness change, velocity and turbulence vary over a distance of 35 to 50 times the water depth. Roughness transition flows show that seiching is lowered by flow non-uniformity. A 1D momentum equation integrating bed friction and drag force exerted by the cylinder array predicts accurately the water surface profile (0.9% mean relative error). The computed profiles show that, upstream of the transition, flow depth varies over a distance of about 2600 times the uniform water depth of the upstream roughness. The 1D equation is solved analytically for zero bed friction.