Regular water environment monitoring is crucial for minimizing contamination caused by waterborne viruses and reducing health risks. As the human adenovirus (HAdV) is linked to clinical episodes of gastroenteritis in children, the present investigation aimed to detect HAdVs in three wastewater treatment plants in Riyadh, Saudi Arabia (King Saud University (KSU-WWTP), Manfoha (MN-WWTP), and Embassy Quarter (EMB-WWTP)). The impact of seasonal variability and meteorological factors on the prevalence of HAdVs was also investigated. The HAdV hexon sequences of the isolated human adenoviruses were phylogenetically analyzed and revealed that the F species of HAdV, especially serotype 41, dominated. The highest prevalence of HAdV was detected in KSU-WWTP (83.3%), followed by MN-WWTP (75%), and EMB-WWTP (66.6%). Seasonal distribution insignificantly influenced the HAdV prevalence among sampling areas (p > 0.05). The highest prevalence of HAdVs (100%) was detected in late Summer and Autumn at temperatures (high: 34–43 °C, low: 18–32 °C) and moderate prevalence of 66.67% in Winter (particularly, in January and February) at lower temperature ranges (high: 26 °C, low: 10 °C–12 °C). The large variation of HAdV prevalence detected at different humidity ranges emphasized the significant impact of relative humidity on HAdV incidence in raw water of WWTPs (p = 0.009, R2 = 0.419). In contrast, wind speed was detected to have insignificant influence on HAdV prevalence among different WWTPs (p > 0.05, R2 = 0.03). The study provides important data for the incidence of HAdVs in wastewater treatments plants in Riyadh, Saudi Arabia, which enabled the successful management of health hazards of viral diseases transmitted via fecal-oral route. In addition, the non-significant influence of seasonal variability on HAdV prevalence highlights the potentiality of utilizing HAdVs as a potential fecal indicator of wastewater contamination.