Good water quality, achieved with environmentally friendly means, is essential in ensuring the safe operation of a dental practice. Our aim was to evaluate procedures and protocols used by dentists for water quality and sustainability. Greek dentists (n = 206) participated in this questionnaire-based study. Statistically significant results (p < 0.05) have shown that (a) female dentists were more interested in additional information about water quality (87.5% vs. 71.8%), had water supply directly from the public network to the dental unit (68.8% vs. 73.8%), were more likely to disinfect surfaces between two appointments (97.7% vs. 88.0%) and were more likely to perform annual maintenance to the dental unit (66.3% vs. 57.9%). (b) More experienced dentists were also more likely to clean the waterline network of the unit with a large amount of fluid once a day (39.3–48.3%), had newer equipment, had more handpieces, and spent more time cleaning and disinfecting the unit (χ2 = 26.21). (c) Dentists who have studied abroad were more likely to perform less strict antiseptic protocols while believing that their practices are environmentally friendly (χ2 = 10.93). Dentists with some postgraduate education were more likely to have an assistant, know the active substance of the antiseptic, supply antiseptic to the handpieces automatically and maintain the dental unit annually (χ2 = 7.24). (d) Dentists who practiced general dentistry were less likely to have an assistant and performed less strict protocols while they cleaned suctions with a large amount of fluid less often (χ2 = 11.64). Dentists who practiced in a clinic (with employees) were more likely to have newer equipment, have an assistant and perform stricter water sustainability protocols. (e) Dentists with a higher annual income were also more likely to have an assistant, perform microbiological tests for the quality of the water of the unit, have a continuous water supply system and perform stricter protocols for water quality of the unit. Overall, less experienced (and younger) dentists are more informed about water quality legislation (27.6%) compared to more experienced and older dentists (13.2–17.5%). Gender, work experience, level of education and dental office characteristics are important factors determining water sustainability, waterlines, and equipment maintenance in dental practice. Dental associations should raise awareness regarding water quality and sustainability, investing in lifelong learning, while implementing protocols and green strategies.