(1) Background: The consequences of iodine deficiency and/or thyroid dysfunction during pregnancy have been extensively studied, emphasizing on infant neurodevelopment. However, the available information about the relationship between iodine, thyroid hormones, and fetal growth in high-risk pregnancies is limited. We aim to investigate if iodine metabolism and/or thyroid parameters can be affected by adverse antenatal/perinatal conditions. (2) Methods: A cross-sectional study examined differences in iodine status, thyroid function, and birthweight between high-risk (HR group; n = 108)) and low-risk pregnancies (LR group; n = 233) at the time of birth. Urinary iodine concentration (UIC), iodine levels in amniotic fluid, and thyroid parameters [thyroid-stimulating hormone (TSH), free thyroxine (FT4)] were measured in mother–baby pairs. (3) Results: There were significant differences between HR and LR groups, free thyroxine (FT4) concentration in cord blood was significantly higher in the LR group compared with HR pregnancies (17.06 pmol/L vs. 15.30 pmol/L, respectively; p < 0.001), meanwhile iodine concentration in amniotic fluid was significantly lower (13.11 µg/L vs. 19.65 µg/L, respectively; p < 0.001). (4) Conclusions: Our findings support the hypothesis that an adverse intrauterine environment can compromise the availability of FT4 in cord blood as well as the iodine metabolism in the fetus. These differences are more noticeable in preterm and/or small fetuses.