Concentrations of major ions in coal mine discharge waters and unconventional hydrocarbon produced waters derived from coal bed methane (CBM) production, are potentially harmful to freshwater ecosystems. Bicarbonate is a major constituent of produced waters from CBM and coal mining. However, little is known about the relative toxicity of differing ionic proportions, especially bicarbonate, found in these CBM waters. As all freshwater invertebrates tested are more acutely sensitive to sodium bicarbonate (NaHCO3) than sodium chloride (NaCl) or synthetic sea water, we tested the hypotheses that toxicity of CBM waters are driven by bicarbonate concentration, and waters containing a higher proportion of bicarbonate are more toxic to freshwater invertebrates than those with less bicarbonate. We compared the acute (96 h) lethal toxicity to six freshwater invertebrate species of NaHCO3 and two synthetic CBM waters, with ionic proportions representative of water from CBM wells across New South Wales (NSW) and Queensland (Qld), in Australia. The ranking of LC50 values expressed as total salinity was consistent with the hypotheses. However, when toxicity was expressed as bicarbonate concentration, the hypothesis that the toxicity of coal bed waters would be explained by bicarbonate concentration was not well supported, and other ionic components were either ameliorating or exacerbating the NaHCO3 toxicity. Our findings showed NaHCO3 was more toxic than NaCl and that the NaHCO3 proportion of synthetic CBM waters drives toxicity, however other ions are altering the toxicity of bicarbonate.