The aim of the study was to determine the impact of the Covid-19 pandemic on the level of physical activity in the last trimester, the risk of developing postnatal depression, and general health habits in late pregnancy and the early postpartum period. Methods: The study population was women 1–8 days postpartum. Participants were divided into three groups depending on when they were recruited: (1) prepandemic (Ppan: n = 252, December 2019–March 2020), (2) COVID1 group (Cov1: n = 262, May 2020–September 2020), and (3) COVID2 group (Cov2: n = 226, June 2021–September 2021). The Ppan group included women from before the pandemic. The Cov1 group included patients after some restrictions were lifted. The Cov2 group included women after vaccinations became available. Research tools included a demographical questionnaire (age, education, childbirth details), the Pregnancy Physical Activity Questionnaire (PPAQ), the Edinburgh Postnatal Depression Scale (EPDS), and the Health Behavior Inventory (IZZ). Results: Regression analysis showed that regardless of other variables, women who gave birth during the pandemic spent less energy on total physical activity compared to the prepandemic group (Cov1: β = −18.930, 95%CI: −36.499 to −1.361; Cov2: β = −26.527, 95%CI: −44.322 to −8.733). We also found that as the risk of depression increased, engagement in general health habits decreased during the pandemic. Conclusions: The Covid-19 pandemic decreased the level of some subdomains of physical activity in pregnant women, with a general negative correlation between emotional state and healthy habits.