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Bacteria often live in dynamic fluid environments^,, and flow can affect fundamental microbial processes such as nutrient uptake^, and infection. However, little is known about the consequences of the forces and torques associated with fluid flow on bacteria. Through microfluidic experiments, we show that fluid shear produces strong spatial heterogeneity in suspensions of motile bacteria, characterized by up to 70% cell depletion from low-shear regions due to ‘trapping’ in high-shear regions. Two mathematical models and a scaling analysis accurately capture these observations, including the maximal depletion at mean shear rates of 2.5–10 s⁻¹, and reveal that trapping by shear originates from the competition between the cell alignment with the flow and the stochasticity in the swimming orientation. We show that this shear-induced trapping directly impacts widespread bacterial behaviours, by hampering chemotaxis …