Vertical slot fishways are increasingly common structures for the passage of a wide variety of migratory fish and contribute to the maintenance of fish diversity in fragmented rivers. These structures are designed with several geometric arrangements and, consequently, flow patterns through them can be shaped to present suitable characteristics for the fish species. To aid in the design of vertical slot fishways, a three-dimensional numerical model was used to simulate the flow for different geometric configurations. An existing vertical slot fishway with nonstandard dimensions was initially modeled and validated. This geometry was used as a reference design. Modifications to the reference design, such as the insertion of cylinders, changes in the baffle shape and position of the vertical slots, as possible rehabilitation measures, were proposed and tested. In summary, five different designs were evaluated with several slopes, totaling 17 geometries. Hydraulic parameters, flow patterns, maximum velocities, velocity fields and turbulence kinetic energy in the pools were analyzed. The results indicate that the maximum velocity values were between 9% and 68% higher than those obtained by the theoretical equation. This indicates that maximum velocities can be underestimated for nonstandard vertical slot fishways if a simplified evaluation is conducted. The insertion of cylinders in the region close to the slot reduces the maximum velocity up to 8.2%. The positioning of the vertical slots on alternating sides increases the maximum values of turbulence kinetic energy and the regions subjected to higher values. However, this configuration provided greater energy dissipation and reduction of velocities by up to 27%. Thus, modifications in nonstandard vertical slot fishways can be useful in future design or rehabilitation of existing structures in order to provide velocities and turbulence more friendly for a higher number of fish species.