Bifenthrin is a pyrethroid insecticide commonly used in agricultural and urban sectors, and is found in watersheds worldwide. As a sodium channel blocker, at sublethal concentrations it causes off-target effects, including disruption of calcium signaling and neuronal growth. At the whole organism level, sublethal concentrations of bifenthrin cause behavioral effects in fish species, raising concerns about the neurotoxic properties of the compound on fish populations. Here we describe the application of a high-throughput behavioral system to evaluate contaminant impacts on the sensitive early-life stages of Delta smelt (Hypomesus transpacificus), a critically endangered teleost species endemic to the San Francisco Bay Delta (SFBD), California, USA. Leveraging the natural behavior of early-larval Delta smelt, whereby they increase movement in bright light and decrease movement in the dark, we developed a test using a cycle of light and dark periods in a closed chamber to test hyper- or hypoactivity for this species. We show that early-larval Delta smelt have a significant preference to move toward light, and utilized the behavioral test to evaluate the impact of exposure to bifenthrin at concentrations found in habitats where Delta smelt reportedly spawn, ranging up to concentrations detected in tributaries to these habitats. All tested concentrations of bifenthrin (nominal 2, 10, or 100 ng/L) caused hyperactivity, over a 96 h exposure, with noted significance determined during the light period of the test. To further understand the impact of bifenthrin exposure, expression of a suite of genes relevant to neurodevelopment, the mechanistic target of rapamycin (mTOR) signaling pathway, and biotransformation in exposed larvae were also measured. Following exposure to picomolar concentrations of bifenthrin, expression of genes in the mTOR signaling and neurogenesis pathways were altered alongside behavior. This study demonstrates how light and dark cycle behavioral tests can be used to assess sensitive alterations in swimming activity in Delta smelt at early developmental stages and how gene expression can complement these assays. This approach can be used to assess the impact of multiple compounds that occur within the restricted habitat of Delta smelt, thus having the potential to greatly inform conservation management strategies for this critically sensitive life stage.