Alterations in zebrafish motility are used to identify neurotoxic compounds, but few have reported how methodology may affect results. To investigate this, we exposed embryos to bisphenol A (BPA) or tetrabromobisphenol A (TBBPA) before assessing larval motility. Embryos were maintained on a day/night cycle (DN) or in constant darkness, were reared in 96 or 24 well plates (BPA only), and behavioural tests were carried out at 96, 100, or 118 (BPA only) hours post fertilisation (hpf). We found that the prior photo-regime, larval age, and/or arena size influence behavioural outcomes in response to toxicant exposure. For example, methodology determined whether 10 μM BPA induced hyperactivity, hypoactivity, or had no behavioural effect. Furthermore, the minimum effect concentration was not consistent between different methodologies. Finally, we observed a mechanism previously used to explain hyperactivity following BPA exposure does not appear to explain the hypoactivity observed following minor alterations in methodology. Therefore, we demonstrate how methodology can have notable implications on dose responses and behavioural outcomes in larval zebrafish motility following identical chemical exposures. As such, our results have significant consequences for human and environmental risk assessment.