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Anthropogenic modification of mangrove systems can lead to decreased habitat quality, potentially affecting food web structure and ecosystem function. Based on carbon and nitrogen stable isotopes, we evaluated the trophic structure of the fish communities from three mangrove systems in southern Baja California, Mexico, subject to varying levels of habitat modification. We hypothesized that anthropogenic habitat modification leads to differences in niche space (and hence trophic structure). We applied a Bayesian approach to the calculation of community level isotope-based metrics of functional trophic structure and compared the results to a structural (Shannon-Wiener) index of diversity. Frequency distributions of stable isotope ratios revealed differences between the highly modified mangrove system and those with limited or no habitat modification. Comparison of the isotopic composition of the dominant fish species sampled in summer and winter indicated limited seasonal differences in this arid region. However, isotope derived metrics of niche space were evaluated in the most highly modified mangrove system, suggesting a greater complexity in nutrient and primary production sources, a higher level of dietary specialization, and low functional redundancy. Fishes from the most pristine mangrove system exhibited highest diversity, a more limited range of isotopic values, and smaller measures of isotopic niche space, indicative of higher trophic redundancy. Comparison of the standardized (baseline-controlled) species-specific isotope ratios indicated that in 37% of cases isotopic differences persisted, further supporting our interpretation of variations in trophic structure. This research highlights that mangrove habitat modification has a marked influence on functional trophic diversity, as well as the fish community structure.