Fishways are structures that aim to achieve the free movement of fish through transversal obstacles in rivers. Despite the wide research about their performance, their hydraulic study and characterization has been so far limited to uniform hydraulic conditions which are usually difficult to reach in natural scenarios, either because inaccurate building or simply because the studied situations during the design of the prototypes are never encountered. This study aims to model pool-type fishways with submerged notches and orifices under different regimens, and uniform and non-uniform performances. For this purpose, the classical formulation used in their design has been modified by studying a real-scale fishway under 29 different hydraulic conditions. The proposed new formulation together with a logical bottom-up iterative calculation is able to predict the observed water level distributions. This study demonstrates that orifices and notches can be considered independently when estimating the water level distribution and discharge through the fishway, and the need to modify the classical formulation. The modeling under non-uniform scenarios will allow to enhance and adapt fishways to achieve a greater fish passage during longer time periods.