While the nanoscale dimensions give metallic nanoparticles unique physical and chemical properties, their potential release in the environment and subsequent effects on ecosystem health are becoming an increasing concern. In the present contribution, for the first time, a novel and simple analytical approach has been developed for the simultaneous quantification of silver and gold nanoparticles (AgNPs, AuNPs) in aqueous samples. The method combines a sample preparation and enrichment step based on cloud point extraction (CPE) with total reflection X-ray fluorescence spectrometry (TXRF) detection. Experimental conditions enabling the simultaneous extraction and detection of AgNPs and AuNPs were studied in detail. Under the best analytical conditions, limits of detection for AgNPs and AuNPs were 0.3 and 0.2 μg L−1, respectively. Due to the lack of suitable certified references materials, accuracy of the CPE-TXRF method was tested by analysing several types of spiked water samples, including mineral, tap, river and sea water. Percentage recoveries achieved for the analysis of spiked samples were in all cases in the range of 82–100% for both types of studied NPs, suggesting that the existence of natural colloids, ionic Ag+ and Au3+ species, and other components in environmental waters have little influence on the quantitative determination of AgNPs and AuNPs. The only exception was the recovery obtained in the analysis of the spiked sea water sample that was around 40–50%. However, for salty aqueous samples, the developed analytical approach might still be feasible if the standard addition method is used for calibration purposes. In an attempt to provide additional information on AgNPs and AuNPs behaviour in the environment, the CPE-TXRF method was also applied to study the influence of organic matter content in waters as well as the influence of soil matrix on AgNPs and AuNPs stability.