This work evaluates the impact of the COVID-19 pandemic on Czech dentistry from March 2020 to March 2021. The assessment was based on questionnaires filled out by 3674 Czech dentists representing 42.6% of practicing dentists in the country. During March–May, 2020 (the first COVID-19 wave), 90.7% of dental practices remained open; however, only 22.8% of the practices continued to operate with no changes, 46.5% had fewer patients, 21.4% treated only acute cases, and 3.8% were closed. During September 2020–May 2021 (the second wave of COVID-19), 96.1% of dental practices remained open, 60.8% operated with no changes, 34.5% had fewer patients, 0.8% treated only acute cases, and 0.5% were closed. The reasons leading to the closure of Czech dental practices during the whole pandemic were a shortage of personal protective equipment (50.5%), a COVID-19 outbreak in the workplace (24.5%), fear of a possible self-infection (24.0%), and quarantine (20.5%). The time range of Czech dental practices closure during the whole pandemic was: 1–2 weeks (49.9%), 2–4 weeks (21.2%), and >1 month (0.8%). The greatest professional difficulties of Czech dentists during the pandemic were crisis operating management (55%), health safety and hygiene concerns (21%), shortage of personal protective equipment (21%), and difficulty working with the protective equipment (15%). In addition, 47.3% of dentists also observed a declining interest in preventive dental care, and 16.9% of them observed worse oral care of patients. These results show that despite the lack of protective equipment, dental care was maintained throughout the pandemic. Additionally, the pandemic negatively affected the patients’ approach to dental care, indicating a deterioration in oral health as a possible delayed outcome of the COVID-19 pandemic.