Field observations have revealed that when water flow is consistently from one direction, seagrass shoots align in rows perpendicular to the primary axis of flow direction. In this study, live Zostera marina shoots were arranged either randomly or in rows perpendicular to the flow direction and tested in a seawater flume under unidirectional flow and waves to determine if shoot arrangement: a) influenced flow-induced force on individual shoots, b) differentially altered water flow through the canopy, and c) influenced light interception by the canopy. In addition, blade breaking strength was compared with flow-induced force to determine if changes in shoot arrangement might reduce the potential for damage to shoots. Under unidirectional flow, both current velocity in the canopy and force on shoots were significantly decreased when shoots were arranged in rows as compared to randomly. However, force on shoots was nearly constant with downstream distance, arising from the trade-off of shoot bending and in-canopy flow reduction. The coefficient of drag was higher for randomly-arranged shoots at low velocities (< 30 cm s- 1) but converged rapidly among the two shoot arrangements at higher velocities. Shoots arranged in rows tended to intercept slightly more light than those arranged randomly. Effects of shoot arrangement under waves were less clear, potentially because we did not achieve the proper plant size?row spacing ratio. At this point, we may only suggest that water motion, as opposed to light capture, is the dominant physical mechanism responsible for these shoot arrangements. Following a computation of the Environmental Stress Factor, we concluded that even photosynthetically active blades may be damaged or broken under frequently encountered storm conditions, irrespective of shoot arrangement. We hypothesize that when flow is generally from one direction, seagrass bed patterns over multiple scales of consideration may arise as a cumulative effect of individual shoot self-organization driven by reduced force and drag on the shoots and somewhat improved light capture.