We assessed area and habitat heterogeneity effects on avian richness and composition in bofedales that differed in size and microhabitat diversity. We analyzed data collected in 2 seasons and 24 bofedales using General Linear Models, Ordinary Least Square models to establish the relationship of predictor variables on richness and Akaike Information Criterion for model selection. We evaluate composition classifying species into groups using Bray Curtis ordination, followed by Multiple Response Permutation Procedure to test for differences among groups, and Indicator Species Analysis to identify species. Bofedales differed in richness (F = 5.1, p < 0.001) and microhabitat diversity (F = 23.4, p < 0.001), but no seasonal differences emerged (p > 0.05). The best model indicates that 54% of variance in richness was explained by area and microhabitat diversity, however, a tendency to decrease in microhabitat diversity as area increases, suggests a relatively more important role of area. Results are supported by composition, as microhabitats not only differed pairwise (T = −94.14, A = 0.601, p < 0.001) and had significant indicator species (p < 0.05), but because its differential contribution to richness, as some microhabitats were more speciose than others. As such, few species-rich microhabitats may contribute more to richness than many species-poor ones which is not predicted by the habitat heterogeneity hypothesis. Disentangling the influence of area and habitat heterogeneity on species richness is important to establish conservation priorities that ensure bofedales integrity under imminent climate change.