By considering chlorpyrifos (CPF), an organophosphorus pesticide with known mechanisms of action that affect neurobehavioral development, we assessed the validity and sensitivity of a miniaturized swim flume by investigating the effects of the insecticide on swimming behavior in medaka (Oryzias latipes) fish growing stages. Medaka in three developmental periods, namely 0, 20 and 40 day-old post-hatch (i.e. time points 0, 20 and 40, respectively), were exposed to CPF (12.5, 25, 50 and 100 μg/L) for 48 h under semi-static conditions. The CPF half-lives during exposures were evaluated and the swimming patterns in a flume section (arena) were presented on two-dimensional gradient maps of forced movement of fish against water current. A comparative numerical analysis of fish residence times between each time point control and the corresponding CPF groups was performed by dividing arenas into 15 proportional areas. The time point 0 control group gradient map showed a noticeably different swim pattern from those of the ≥12.5 μg CPF/L groups, which was statistically supported by the differences for residence times seen in ≥12 corresponding areas. The control group gradient maps for time points 20 and 40 differed from those of the respective ≥12.5 μg CPF/L groups. The comparative analysis of the residence times in the corresponding 15 areas revealed differences in ≥5 areas for time point 20 and in ≥3 areas for time point 40. The integrative analysis of the gradient maps and the numerical statistics revealed stage-specific effects and a concentration-response relationship between CPF and alterations on forced medaka swimming despite the dissipation of CPF from the water column. These results indicate the validity of the miniaturized swim flume toward a more environmentally realistic scenario for the evaluation of neurodevelopmental and behavioral toxicity in small fish models.