The use of small aquatic model organisms to investigate the behavioral effects of chemical exposure is becoming an integral component of aquatic ecotoxicology research and neuroactive drug discovery. Despite the increasing use of invertebrates for behavioral phenotyping in toxicological studies and chemical risk assessments, little is known regarding the potential for environmental factors—such as geometry, size, opacity and depth of test chambers—to modulate common behavioral responses. In this work, we demonstrate that test chamber geometry, size, opacity and depth can affect spontaneous, unstimulated behavioral responses of euryhaline crustacean Artemia franciscana first instar larval stages. We found that in the absence of any obvious directional cues, A. franciscana exhibited a strong innate wall preference behavior. Using different test chamber sizes and geometries, we found both increased wall preference and lowered overall distance traveled by the test shrimp in a smaller chamber with sharper-angled vertices. It was also determined through quantifiable changes in the chambers’ color that the A. franciscana early larval stages can perceive, differentiate and react to differences in color or perhaps rather to light transmittance of the test chambers. The interaction between innate edge preference and positive phototaxis could be consistently altered with a novel photic stimulus system. We also observed a strong initial preference for depth in A. franciscana first instar larval stages, which diminished through the acclimatization. We postulate that the impact of test chamber designs on neurobehavioral baseline responses warrants further investigation, in particular considering the increased interest in behavioral eco-neurotoxicology applications.