Structural dynamic and fluid flow analysis of positive displacement piezoelectric micropumps are carried out for microfluidic water transport applications. The micropump consists of trapezoidal prism inlet/outlet elements; the pump chamber; a thin structural layer and a piezoelectric transducer element. Governing equations for the flow fields; the structural piezoelectric bi-layer membrane motions and electrical variables are considered. Two-way dynamic coupling of forces and displacements between the solid and the liquid domains in the systems are considered. The effects of the structural layer material selection and the thickness of thin structural layer on the structural deformation and fluid flow are investigated. The variation the structural layer material and its thickness enable the selection of the best micropump design among the investigated micropumps made of silicon and Pyrex glass while other parameters are kept unchanged. The change of the structural layer material is considered here through the variation of density, Young's modulus and Poisson's ratio. Optimum membrane thickness is also investigated aiming to generate higher rates of time-averaged flow for the selected micropump structural layer material. The present study is useful in the implementation of the micropumps into lab-on-a-chip microfluidic systems.