In the present work, a simple, sensitive method was developed for the determination of beryllium and chromium by electrothermal atomic absorption spectrometry (ETAAS) after simultaneous pre-concentration by cloud point extraction (CPE). The procedure was based on the formation of the hydrophobic chelates of Be and Cr(III) and/or Cr(VI) with cupferron, followed by their quantitative extraction into the surfactant-rich phase by the Triton X-114. The effects of the main parameters affecting the extraction recovery of CPE, such as pH of the sample solution, concentration of the chelating agent and surfactant, equilibration temperature and incubation time, were investigated and optimised. Under the optimal experimental conditions, the limits of detection and limits of quantification for Be were 0.33 and 1.11 pg and for Cr(VI) were 0.98 and 3.28 pg, respectively. The pre-concentration factor for Be and Cr(VI) was found to be 20 for 10 mL of the water sample. The accuracy of the method was confirmed by analysis of certified reference materials of waters (“Trace Metals in Drinking Water” and SRM 1643e “Trace Elements in Water”) with satisfactory results. The method developed was successfully applied to the pre-concentration and determination of trace quantities of beryllium and chromium(VI) in different natural waters.