<p>Access to safe drinking water remains a major public-health challenge in arid regions such as Jordan, where privately operated desalination plants increasingly supplement limited municipal water supplies. This study evaluated microbial contamination patterns in desalinated drinking water collected from 27 private treatment plants in Mafraq Governorate, Jordan. A total of 169 water samples, including dispensed tap water collected directly from dispensing outlets (<i>n</i> = 73), bottled water (<i>n</i> = 32), and refillable gallon water (<i>n</i> = 64), were collected across four seasonal sampling rounds and analyzed in triplicate for <i>Escherichia coli</i>, <i>Pseudomonas aeruginosa</i>, total coliforms, and fungal contamination. Residual free chlorine concentrations were also measured on-site. Because microbial outcomes exhibited sparse positive detections and substantial zero inflation, triplicates were aggregated at the sample level. Microbial outcomes were analyzed as binary detection variables using generalized linear mixed models and Firth penalized logistic regression. Refillable gallon water exhibited the highest overall contamination frequency (25.0%), followed by bottled water (10.2%) and dispensed tap water (4.1%). Relative to dispensed tap water, refillable gallon water demonstrated significantly greater odds of total coliform contamination (OR = 13.24, 95% CI: 3.72–47.13) and fungal contamination (OR = 11.41, 95% CI: 3.80–34.22). No significant overall seasonal variation was observed across most microbial indicators, although <i>Pseudomonas aeruginosa</i> exhibited significantly greater detection odds during June relative to September (OR = 4.64, 95% CI: 1.17–18.41). These findings highlight the importance of strengthening operational hygiene practices and improving microbial monitoring in private desalinated water systems, particularly refillable gallon water pathways.</p>