Natural bedrock rivers have various bedforms created by erosion. Flow‐parallel incisional grooves formed longitudinally in bedrock are one common example of such bedforms. Although several studies have been conducted regarding these grooves, their formation processes are not well understood. In this study, we conducted a flume experiment to investigate the relationship between the flow structure and longitudinal grooves. The experimental results strongly suggest that longitudinal grooves are formed by moving sediment concentrated in multiple longitudinal pathways by turbulence‐driven secondary flows. The sediment preferentially abrades the bedrock along these flow‐parallel pathways resulting in longitudinal grooves in the bedrock. Measurements of the flow velocity distribution show that the positions of secondary flow cells producing the initial formation of the grooves are altered by the formation of those grooves. Because displaced secondary flows tend to make the sediment collide with the sidewalls of the longitudinal grooves, the grooves grow wider over time and some grooves partially combine with other adjacent grooves. The initial maximum number of longitudinal grooves N_max strongly depends on the river width‐depth ratio B/D, which defines the number of secondary flow cells, and can be expressed as N_max = 0.5B/D. However, because some grooves coalesce with other grooves due to the effects of the displacement of secondary flows, the average number of grooves showed a relationship that can be expressed as N = 0.41B/D. Based on this relationship, we inversely estimated the flow discharge of the Abashiri River using the number of longitudinal grooves observed in the river. The result was consistent with the observed annual maximum flow discharge of the river. This suggests that the number of longitudinal grooves can be used as an indicator for estimation of the formative flow discharge in bedrock rivers.