Juvenile Pacific abalone (Haliotis discus hannai Ino) are currently reared in land‐based aquaculture systems until they reach the necessary size for seeding in the sea. One problem that this industry faces is that an uneven distribution of juveniles in tanks can lead to variations in the growth rate. Understanding the cues that affect the sheltering behaviours exhibited by juvenile Pacific abalone—namely, the food distribution and the water flow velocity—will help optimize abalone culture settings. In this study, a group of 1,000 juvenile Pacific abalone (distributed across three tanks) was visually observed and enumerated during six experiments that were conducted over a 5‐month study period. It was found that juvenile Pacific abalone preferred to shelter close to food sources when the food was unevenly distributed. When the food was evenly distributed, the juveniles tended to avoid areas of rapid water flow and distributed evenly across the sheltered areas receiving the equal water velocity. This distribution might be the confounding effects between water flow velocity and food stimulus. Based on these findings, it was recommend that the food and water velocity be evenly distributed in an abalone aquaculture system.