Substance use during pregnancy is highly prevalent worldwide leading to a spectrum of lifelong neurobehavioral consequences. One of the most commonly observed effects of prenatal substance use is an increased risk of emotional processing deficits and developing an affective disorder, particularly anxiety and depression, with evidence of symptoms emerging in infancy and both persisting and becoming increasingly exacerbated into adulthood. Among the various substances misused during pregnancy, alcohol, nicotine, cannabis, and opioids have been noted as the most commonly used for a variety of reasons. Despite the legal status of these substances, it is evident that prenatal exposure to alcohol, nicotine, cannabis, and opioids produces a myriad of neurobiological alterations that may underlie the development of negative affective behaviors in the offspring. This chapter discusses the existing clinical and preclinical (using animal models) literature that has identified the spectrum of negative affective behaviors and associated neurobiological alterations across the lifespan resulting from prenatal exposure to these specific substances.