Dysfunctions of the brain’s serotonin system are thought to underlie the symptoms of depression and autism spectrum disorder (ASD); the former is thought to be underpinned by a decrease in serotonin signaling and the latter an increase. However, because the roles of serotonin in the brain during health and disease are ill defined, it is extremely challenging to investigate these hypotheses with an eye towards therapies. This situation is confounded because current therapies assume that the serotonin system dysfunctions in the same way regardless of the multitude of causes (psychological, genetic, exposure, disease) of human disease. In this work, we develop and utilize novel voltammetric tools and combine them with mathematical models and confocal imaging to characterize serotonin neurotransmission in different animal models of depression and ASD. We find characteristic chemical serotonin phenotypes that underlie the two disorders. We model the experimental data and offer mechanistic insights into how different extracellular mechanisms that regulate serotonin circumstantially dysfunction. These insights lead us to suggest novel treatment strategies.