Study about the mechanical energy balance and the energy loss of 3-D turbulent flows in open-channels has its own complexities. The governing equation of the mechanical energy in turbulent flows has been previously known and includes turbulence parameters that their calculations or measurements are not easy. In this study, a form of the total mechanical energy equation that leads to a number of significant physical insights is analytically investigated, from which analytical relationships for the energy loss estimation in 3-D turbulent flows are defined. The effect of different turbulence parameters is reflected on the new relationships and analyzed by equalizations replacing unknown correlations with closure approximations using the numerical turbulence simulation. In order to investigate the application of the analytical relationships, numerical simulations are performed by using OpenFOAM software to solve the Navier-Stokes equations with the RSM turbulence model in open-channels with different geometries. Then, the contribution of the turbulence parameters to the total mechanical energy balance is evaluated in uniform and nonuniform turbulent flows and their difference is analyzed, that leads to identify the parameters affecting the friction and local losses. The results demonstrate that the magnitudes of the turbulent diffusion, the work done by the viscous stresses pertaining to the mean motion and the viscous diffusion of the turbulence energy are substantially smaller than the other terms of the total energy equation for turbulent flows in open-channels with different geometries, while the effect of the variations of the turbulence kinetic energy and the work done by the turbulence stresses, that has not been considered in the previous mechanical energy equations, is more important in complex flows. From a practical viewpoint, in order to study the details of the total mechanical energy balance and the energy loss in 3-D turbulent flows with the presence of the secondary currents, the proposed method can be useful.