Boundary effects on the stability of the street of longitudinal vortices with their alternately changing direction are investigated by using the vortex filament model. The analysis shows that the longitudinal vortex street is unstable to a infinitesimal disturbance in both the infinite and the semi-infinite regions over a flat bed, whereas it is stable in the finite region bounded by the free surface and the flat bed. These results were recognized to correspond with the behavior of longitudinal vortices experimentally found in both the inner and the outer layers of an open channel flow. Furthermore, arrangements of a vortex generator are investigated to control longitudinal voricies, sand wave and bed load.