The flowrate in hydraulic turbines can be measured using the pressure-time method specified by the IEC 60041 standard. This method assumes a one-dimensional (1D) flow and is limited to straight pipes with a uniform cross section and specific restrictions on length (L > 10 m) and velocity (U × L > 50 m2 s−1). However, in low-head hydropower plants, the intake typically has a variable cross section and small length, making it challenging to use this method. This paper presents the development of a methodology that extends the applicability of the pressure-time method for variable cross section by using three-dimensional computational fluid dynamics (3D CFD). A combination of 3D CFD and 1D pressure-time methods is employed iteratively to estimate the kinetic energy correction factor. The obtained time-dependent values are then used in the 1D pressure-time method to calculate the flowrate. The new methodology is applied with experiments performed on a test rig with a reducer. The obtained results illustrate the significantly different kinetic energy correction factor obtained than those obtained using constant or quasi-steady assumptions. The proposed methodology changes the mean deviation compared to the reference flowmeter from −0.83% (underestimation of flowrate) to ±0.1%, increasing the method's accuracy.