Turbidity levels in rivers increase from changes in water flow or high recreational use, which reduces visibility and affects the use of visual cues by aquatic organisms. Decreased visibility affects time spent associating with conspecifics and strength of preference (SOP) in fish that use visual cues. Here, we test the hypothesis that fountain darter (Etheostoma fonticola; a federally endangered species) body size preferences are affected by reduced visibility. We tested offspring of wild-caught fish using a dichotomous choice design with clear and reduced visibility treatments. Males and females spent more time associating with fish of the opposite sex in the clear treatment than in the reduced visibility treatment. Smaller females spent more time associating with other females in the clear treatment, whereas larger females spent more time associating with other females in reduced visibility. Smaller females had a higher SOP for larger males in the clear treatment, whereas larger females had a higher SOP for larger males in the reduced visibility treatment. Increased levels of turbidity that leads to reduced visibility affect the use of visual cues in E. fonticola, resulting in a reduction in time spent in social interaction and affecting association preferences of this endangered species.