Acute gastroenteritis (AGE) is a major contributor to pediatric morbidity and mortality worldwide. There is a scarcity of data on AGE in North Lebanon, a region profoundly affected by the Syrian refugee crisis and water sanitation issues. This study examines the prevalence, risk factors, and seasonal variations in adenovirus and rotavirus infections in children with AGE in North Lebanon. A cross-sectional study was conducted from September 2022 to August 2023 on 400 children (1 month to 5 years old) with AGE that were admitted to pediatric departments of three private hospitals in North Lebanon. Stool samples were collected and tested using chromatographic immunoassays. Comprehensive demographic and clinical data were collected and analyzed. Rotavirus was the most frequent viral agent (28%), followed by adenovirus (12.3%) and mixed infections (5.5%). Rotavirus vaccination demonstrated a significant protective effect, and lower infection rates were associated with breastfeeding and consumption of bottled water (p < 0.001). Higher infection rates correlated with lower levels of maternal education and household incomes (p < 0.001). Malnutrition significantly increased susceptibility to rotavirus infections (p < 0.001). This study emphasized the urgent need for targeted public health interventions in North Lebanon to mitigate the burden of rotavirus and adenovirus-induced acute gastroenteritis among children.