Experiencing a hurricane during pregnancy is associated with increased risk of adverse birth outcomes and poor mental health. Pregnant people from marginalized communities are more susceptible to adverse effects, as they have fewer resources to overcome hardships at a time when shelter and nutrition are essential. When Hurricane Maria (HM) devastated Puerto Rico in September 2017, the archipelago was already burdened with high poverty, health disparities, environmental contamination, and fragile utility infrastructure. We aimed to compare biomarkers of environmental exposures among pregnant participants in the PROTECT cohort before and after HM and to identify hurricane-related sources of exposure. Metals, PAHs, phthalate metabolites, and phenols were measured in urine samples collected from participants at three prenatal visits (2011–2019). Samples were categorized as before, <3 months, 3–6 months, and >6 months after HM. Using linear mixed effects models, we found that in the 6 months after HM, participants had higher Co, Ni, and DEHPTP concentrations, indicating increased exposure, and lower concentrations of PAHs, several metals, and phthalates, suggesting decreased exposure, compared to pre-HM levels. Biomarkers were not associated with potential exposure sources assessed through questionnaire or previously measured tap water contaminants. This study provides insight into how extreme weather events may alter environmental exposures among pregnant people in Puerto Rico. As climate change has increased the frequency and magnitude of such events, additional research is needed to clarify the implications for maternal and child health and to identify sources of related environmental exposures within this vulnerable population.