University students are regarded as the backbone of society, and their mental health during a pandemic may have a substantial impact on their performance and life outcomes. The purpose of this study was to assess university students' mental health, specifically depression, anxiety, and stress, during Lebanon's extended COVID-19 pandemic, as well as the sociodemographic factors and lifestyle practices associated with it. An online anonymous survey assessed the rates of mental health problems during COVID-19, controlling for socio-demographics and other lifestyle practices, in 329 undergraduate and graduate university students. Instruments utilized were the Patient Health Questionnaire (PHQ-9) for depression, the Beck Anxiety Inventory (21-BAI) for anxiety, and the Perceived Stress Scale (PSS-10) for stress. The study employed descriptive statistics and multiple logistic regression models to analyze the association between depression, anxiety, and stress with sociodemographic and lifestyle factors. Results were evaluated using adjusted odds ratios and confidence intervals, with a significance level of 0.05. Moderate to severe rates of depression, anxiety and stress among students were reported by 75.9%, 72.2%, and 89.3%, respectively. The odds of anxiety and stress were higher among women compared to men. Students who used private counseling services had higher odds of anxiety and stress than those who did not. Overall rated health was a major predictor of depression and anxiety, with the "poor" and "fair" overall-reported health groups having higher odds than the "Excellent" group. When compared to those who did not smoke, students who increased their smoking intake had higher odds of depression, anxiety and stress. Students who reduced their alcohol consumption had lower odds of anxiety compared to those who did not consume alcohol. Students who reduced their physical activity had higher odds than those who increased it. Finally, students who slept fewer than seven hours daily had higher odds of depression than those who slept seven to nine hours. Our findings indicate a national student mental health crisis, with exceptionally high rates of moderate to severe depression, anxiety, and stress. Factors such as gender, university program, overall rated health, importance of religion in daily decisions, private counseling, smoking cigarettes, alcohol consumption, physical activity, and sleeping, were all found to have an impact on mental health outcomes. Our study highlights the need for university administrators and mental health professionals to consider targeted mental health programming for students, particularly for women and those with poor or fair overall perceived health.