Environmental factors can directly influence phenotype such that a tight correlation between morphological and environmental variation is expected. However, morphological response to environmental variation may also reflect constraints imposed by interactions between adjacent structures such as the gills and the trophic apparatus in fishes. Such complex interactions help to explain why an organism's phenotype may appear mismatched with its environment. This study quantified relationships between morphological traits related to feeding and respiration and the physico-chemical environment in a widespread cichlid fish Astatoreochromis alluaudi, from six sites in Uganda. This species is known to be plastic in jaw morphology with enlarged jaw morphs specialized for mollusk eating, and reduced jaw morphs for insect eating. However, recent studies suggest a mismatch between the trophic morphology and feeding ecology in field populations of this species that could reflect interactions with the branchial apparatus; the development of large gills in low-oxygen habitats may constrain or affect pharyngeal jaw size. MANCOVA results for morphometric data showed a strong population effect for both gill and jaw traits. We found a significant negative correlation between composite morphological variables (principle components) relating to the size and shape of gill apparatus and pharyngeal jaw size across all populations. Furthermore, gill traits generated from principle component analysis were positively correlated with water conductivity, which was highly correlated with dissolved oxygen (DO) across the six sites. These results suggest that a particular morphological trait (pharyngeal jaw size) can be indirectly altered by the physico-chemical environment (conductivity and DO) due to correlated effects on a functionally unrelated morphology (gill size). These results have important implications for understanding species distribution patterns because trade-offs between suites of traits may constrain an individual's ability to exploit an otherwise suitable habitat or resource.