To address water scarcity, the Cyprus government adopted a multifaceted water development strategy of collecting, producing, recycling and conserving water, under strict national legislative control and in compliance with EU directives. The official monitoring of surface and recycled water builds on a holistic approach, which includes chemical, ecotoxicological and microbiological (in the case of recycled water) testing. This work describes the introduction of genotoxicity and mutagenicity testing in the holistic monitoring of water quality in Cyprus. Recycled, surface, ground and drinking water samples were assessed for genotoxicity and mutagenicity via bacterial reversion tests, using the SOS-Chromo Test (TM) kit and two kits based on the well known "Ames test" kits, namely the Muta-Chromo Plate (TM) kit and the Ames MPF (TM) Mutagenicity 98/100 AQUA kit. In addition, toxicity was assessed using the Microtox (R) test and the Daphtoxkit F (TM) magna kit. Overall, water samples found to be mutagenic were not necessarily positive for toxicity. It was also notable that the SOS-Chromo Test (TM) kit, developed to evaluate the primary response to cell damage measured by promoter activity of the SOS-repair genes did not detect any genotoxicity in the samples tested, despite a positive mutagenicity result in some of the samples via the Muta-Chromo Plate Test (TM) kit. Finally in a pilot investigation, the Microtox (TM) test, the SOSChromoTest (TM) and the Muta-Chromo Plate (TM) test were employed to test the hypothesis that under high temperature and sunlight, conditions that prevail during the hot Mediterranean summers, bottled drinking water may become contaminated with hazardous compounds from the plastic package. Overall, the results demonstrate the importance of incorporating a mutagenicity test in the holistic monitoring of water quality.