Coloration and color vision covary with lighting in many taxa. Determining the mechanisms underlying these patterns is difficult because lighting environments can have multiple effects on signaling that occur at multiple time scales. Lighting environments can (1) immediately affect signal propagation and transmission which determine the radiance spectrum reaching the receiver, (2) induce variation in visual systems via developmental plasticity, and (3) lead to genetic differences in visual systems due to a history of selection in different habitats. We tease apart these effects on pecking preference and examine the relationship between pecking preference and opsin expression. Using killifish from two visually distinct populations (clear vs. tea-stained water), we performed crosses (genetics), raised animals under different lighting conditions (developmental plasticity), and assayed preference to peck at different colored dots under different lighting conditions (immediate effects). Pecks are interpreted as foraging preference. Developmental plasticity affected both pecking preference and opsin expression. Lighting environments also had immediate effects on pecking preference, but these depended on the lighting conditions animals experienced during development. Genetic effects were detected in opsin expression, but there were no corresponding effects on pecking preference. Overall, only 3.36% of the variation in pecking preference was accounted for by opsin expression.