Abstract Background Research indicates that mental health worsened during the Coronavirus crisis, in particular among women and university students. However, few longitudinal studies have so far investigated the changes in mental health outcomes across three subsequent waves of the COVID-19 pandemic. Therefore, this study aims to examine changes in mental health among university students. Methods A total of 1,961university students from Poland, at mean age 23.23 years (SD = 3.16, 57.47% of women) were included in this repeated cross-sectional study across three waves of the COVID-19 pandemic: W1 (n = 657), W2 (n = 654), and W3 (n = 650). They completed the online survey with the Generalized Anxiety Disorder (GAD-7), Perceived Stress Scale (PSS-10), General Self-Rated Health (GSRH), and Satisfaction with Life Scale (SWLS), as well as sociodemographic variables. Results The prevalence of people at high risk of anxiety and perceived stress, poorer physical health, and low life satisfaction changed significantly across three waves of the COVID-19 pandemic. The results of the two-way ANOVA showed that both the wave (W1<W2<W3) and gender (men<women) had a significant impact on the level of anxiety. Statistically significant changes in perceived stress were found between pandemic waves (W1>W2, W1>W3), and genders (men<women). Self-reported physical health significantly deteriorated in W3 compared to W1 and W2 (W1>W3, W2>W3), and was significantly worse in women than in men. The level of life satisfaction also decreased significantly in W3 (W1>W3, W2>W3), but did not differ between men and women. High GAD risk was presented two times more frequently among women and people who subjectively assessed their health as poor, three times more likely in participants dissatisfied with their lives, and seven times more probably in persons with high-stress levels. Conclusions The results of this study consistently indicate (using parametric and non-parametric statistical analysis) that there are significant differences in mental health problems across three waves of the COVID-19 pandemic. It suggests that pandemic waves should be considered in future review studies and meta-analyses. Furthermore, these findings indicate a potential role for prevention and intervention programs aimed at alleviating life satisfaction and subjective assessment of health and improving coping skills to reduce stress and anxiety.