The COVID-19 pandemic has posed unique academic, social, financial, and health-related challenges for young adults. While numerous studies have documented average increases in reported mental health issues in the general population, few have measured the magnitude of changes in mental health symptoms and sleep difficulties within individuals. Here, we measure the impact of the COVID-19 pandemic on mental health and sleep of university students pre- and mid-pandemic. Prior to the pandemic (Fall 2019), individuals (n = 23) were recruited to participate in an eight-day, comprehensive sleep study using Fitbit® actigraphy. Participants also completed detailed mental health and sleep surveys, including depression (BDI-II), anxiety (STAI), and sleep disturbance (PROMIS) surveys. One year later, these individuals repeated the study during the pandemic (Fall 2020); participants completed the original surveys and sleep study, in addition to a targeted survey on mental and sleep health due to the pandemic. Self-reported levels of anxiety, depression, and sleep disturbance, and sleep parameters, measured by actigraphy, were compared within the same individuals pre- and mid-pandemic. Self-report survey data revealed that three-quarters of participants experienced an increase in stress and anxiety due to the pandemic. In addition, intra-individual depression and anxiety symptoms increased to clinically significant levels within individuals from pre- to mid-pandemic. Over two-thirds of participants reported sleeping less, and more than half reported that their sleep health had worsened during the pandemic. Changes in sleep disturbance were positively associated with changes in depression and anxiety, reinforcing the robust relationship between poor sleep quality and mental health. Furthermore, individuals who reported greater sleep disturbance during the pandemic experienced lower relative proportions of both REM and deep sleep. The impact of the COVID-19 pandemic on university students is multi-faceted-mental health, sleep quality, and the amount of restorative sleep are negatively affected by the pandemic environment. These compounded effects exacerbate the health consequences of the pandemic and highlight a need for increased attention to the prevention and treatment of mental health disorders, particularly in vulnerable populations of young adults.