In this work we have developed a Total reflection X-Ray Fluorescence (TXRF) based methodology for the determination of uranium in natural water samples at ultra-trace concentration level. The methodology involves functionalization of quartz sample supports used for TXRF measurements with (3-Amidoxy) triethoxysilane, which has very high uranium uptake efficiency. (3-Amidoxy) triethoxysilane has been synthesized from (3-Cyanopropyl) triethoxysilane (CPTS). This amidoxime functionalized sample supports, simply needed to be dipped in the uranium solution for 3 h after which, it can be directly taken for TXRF measurements. The developed methodology is very fast, simple with less sample preparation steps involved. The present work utilizes Rayleigh scattered peak to construct the calibration curve for the quantification purpose. The developed methodology has improved accuracy as well as precision for the quantification of uranium at such low concentrations level. The detection limit and accuracy obtained are 0.013 ng/mL (13 ppt) and 1.9%, respectively which are the lowest using any X-Ray Fluorescence based method, to the best of our knowledge. The method was successfully applied for the U determination in natural water samples like ground water, river water and sea water.