Most obstetrical studies have focused on maternal response to the SARS-CoV-2 virus but much less is known about the effect of COVID-19 on fetal physiology. We aimed to evaluate the effect of the maternal SARS-CoV-2 infection on the fetal homeostasis with the use of detailed ultrasonography and echocardiography and consideration of the effect of vaccination. This was a multi-center study of fetuses who had prenatal detailed ultrasound and echocardiographic examinations performed by fetal cardiology specialists. The subjects were divided based on the COVID vaccination status (vaccinated women who did not have COVID-group V, unvaccinated women who had COVID-group UV, and unvaccinated women who did not have COVID-control group). We evaluated the ultrasound and echocardiography results obtained. The study group included 237 gravidas from four prenatal cardiology centers. In the group of fetuses with normal heart anatomy, normal cardiovascular function had 147 (81%) fetuses and functional cardiovascular anomalies were present in 35 (19%) cases. Functional cardiovascular anomalies were present in 11 (16%) fetuses in the V group, 19 (47%) fetuses in the UV group and 5 (8%) fetuses in the control group (p < 0.01). There were 56 (24%) fetuses with extracardiac anomalies. Extracardiac anomalies were present in 20 (22%) fetuses in the V group, 22 (45%) fetuses of the UV group and in 14 (14%) fetuses in the control group (p < 0.01). Our study has proved that maternal COVID-19 infection can affect the fetal physiology and mild cardiac and extracardiac markers detected by fetal ultrasonography and echocardiography. Moreover, maternal vaccination results in lower occurrence of these findings in fetuses.