It is well established that changes to the chemical environment can impair development, physiology and reproductive biology; by contrast, impacts on communication have not been widely reported. This is surprising given that chemical communication is the most widely used sensory modality in nature, and that variation in the chemical composition of the environment is the rule, not the exception. Here, we show that chemically mediated species recognition in a swordtail fish, Xiphophorus birchmanni, can be hindered by anthropogenic disturbance to the signalling environment. Females have a strong preference for conspecific male chemical cues, yet they hybridize in nature with the congener X. malinche. Wild-caught females showed a strong preference for conspecifics when tested in clean water, but failed to show a preference when tested in stream water subject to sewage effluent and agricultural runoff. We hypothesized that this was due to the interaction between chemical communication systems and humic acid (HA), a ubiquitous, natural product elevated to high levels by anthropogenic processes. When exposed to elevated concentrations of HA, female X. birchmanni again lost their preference for conspecific male chemical cues, while visual mating preferences and motivation to mate were retained. Sub-lethal concentrations of seemingly benign substances can thus have a drastic effect on natural populations through their specific impact on communication systems.