Many environmental flows can be considered as shallow. The effects of shallowness are reflected in a strong influence of bed friction and in horizontal velocity gradients as a result of variations in bathymetry and roughness. The horizontal length scales, being generally larger than the vertical length scales, dominate the flow pattern through horizontal momentum exchange. However, three-dimensional effects do play an important role as non-uniformity of bed roughness gives rise to secondary circulation driven by turbulence anisotropy. This not only results in vertical motion, but also hampers the development of eddies formed in the horizontal shear layers. This chapter addresses a few examples where the flow structure is affected by groynes, and examples where roughness variations are the dominant mechanisms creating horizontal shear layers. In the latter cases, the contribution of secondary circulation to horizontal momentum transfer cannot be neglected, demonstrating the importance of three-dimensional effects in shallow flows.