Optical coherence tomography (OCT) offers high-resolution, three-dimensional (3D) imaging of semi-transparent media, including biological samples, in a swift manner. Its operation in the near-infrared spectrum ensures non-invasive and non-destructive imaging, making OCT advantageous for diverse applications spanning biology, biomedical science, agriculture, and material science. We introduce a compact OCT microscope prototype tailored for field assessments in aquatic animal study. Specifically, it is used to evaluate pesticide exposure in freshwater fish. The prototype, comprising exclusively commercial optical components, achieves imaging depths up to 2 mm from a sample’s surface at a rate of 20 frames per second and boasts resolutions of 10 μm both laterally and in depth. We demonstrated its utility by imaging African catfish exposed to the herbicide 2,4-D dimethylammonium, comparing these with control samples. We performed in vivo 3D imaging, using the developed prototype, on each catfish throughout its hatching and embryonic development period, comparing the 2,4-D exposure with the control. The results show significant deviations in the exposed group from the typical developmental patterns observed in the control group. This confirms the capability of OCT to assess the effects of herbicides on aquatic organisms.