This paper presents the variation in key flow properties due to the standard deviation of obstruction shape variation in nature-like fishways, using a Godunov type numerical method of two dimensional shallow water equations. Elliptic obstructions having different aspect ratios are embedded in the model fishway. The variation of shape is evaluated from the standard deviation of diameter length. The change in flow parameters because of the increment in the standard deviation of shape variation was compared from four different test cases. The increment in the standard deviation showed a distinct effect on the flow parameters. Increase in standard deviation showed the decrease in the area occupied by higher velocities, as well as increase in variation of flow velocities. Likewise, the increase in standard deviation raised the average water depth in the fishways.