Many single- and multi-phase fluid dynamical systems are governed by non-linear evolutionary equations. A key aspect of these systems is that the fluid typically flows across spatially and temporally varying cross-sections. We, first, show that not any choice of state- variables may be apt for obtaining a port-Hamiltonian realization under spatially varying cross- section. We propose a modified choice of the state-variables and then represent fluid dynamical systems in port-Hamiltonian representations. We define these port-Hamiltonian representations under spatial variation in the cross-section with respect to a new proposed state-dependent and extended Stokes- Dirac structure. Finally, we account for temporal variations in the cross-sectio...