The aim of the present study is to understand the turbulent flow for various configurations of vertical slot fishways and to determine how their characteristics might be modified in order to facilitate the passage of small species. A cylinder is used to change flow structures in the fishway model. Proper Orthogonal Decomposition (POD) of velocity fields acquired by Particle Image Velocimetry (PIV) is achieved to analyze the effects of the vertical cylinder within the pools, on the dimensions of recirculation zones, the turbulence intensity and the spatio-temporal evolution of the flow.