Packing material can release certain elements such as As, Cr, or Sb into its content and, thus, contaminate the drinking water. The effect of As, Cr, and Sb on human health depends highly on the chemical species in which these elements are introduced into the body. For the above reasons quantification and speciation of As, Cr, and Sb in flavored and functional drinking water samples is an important issue. Total, inorganic, and organic species of As, Cr, and Sb including As(III), As(V), Cr(VI), Sb(III), and Sb(V) were studied in flavored and functional drinking waters. Analyses of total As, Cr, and Sb were conducted using inductively coupled plasma mass spectrometry (ICP-MS) according to ISO 17294-2:2016. The speciation analysis of arsenic, chromium, and antimony in bottled flavored and functional drinking waters was conducted with the use of the elemental (HPLC/ICP dynamic reaction cell (DRC) MS) and molecular (electrospray ionization MS/MS) mass spectrometry. Concentrations of total As, Cr, and Sb (µg∙L−1) in waters studied were in the ranges 0.0922 ± 0.0067 to 8.37 ± 0.52, 0.0474 ± 0.0014 to 1.310 ± 0.045, and 0.0797 ± 0.0026 to 1.145 ± 0.019, respectively. Speciation analysis showed that, apart from the toxic ionic species, known and unknown organic species were present in test samples. The risk assessment results proved that there is no risk associated with consumption of these tested beverages in terms of the non-carcinogenic effect of total and inorganic or organic species of As, Cr, and Sb.