Substance use during pregnancy is common, costly and associated with maternal and newborn health consequences. Assessment of substance use should be integrated into prenatal care. Substance use identification methods include patient interview, screening instruments, and biological testing. In this review, we critically evaluate screening and testing for substance use during pregnancy, highlighting the benefits and barriers of integrated assessment into prenatal care. We also discuss the limitations and negative consequences that should be considered when implementing screening and/or testing procedures. Lastly, we provide recommendations for the ethical implementation of screening and testing for substance use in the context of prenatal care.