Studies that evaluate conservation status of ecosystems in Mexico often lack the integration of some theoretical bases as well as some methodological tools that landscape ecology offers. This situation imposes limitations for the implementation of more adequate management, restoration and conservation strategies. In this study we propose a four stage method in order to characterize the biophysical environment and to estimate the vegetation conservation status in a highly environmentally heterogeneous basin, under strong anthropogenic pressure. The stages were: 1) delimitation and characterization of environmental units based on biophysical conditions, 2) quantification of vegetation structure and composition, 3) classification of the species according to their functional responses, and 4) evaluation of the conservation status based on the community structure and composition. As a result, biophysical units showed differences in richness, diversity, and in the importance index values of native, weed and introduced species. Plant functional groups were identified; they comprised different environmental responses in a conservation gradient in the biophysical units. Through the canonical correspondence analysis, it was demonstrated that composition is mainly related to the light regime, temperature, humidity and some soil conditions. Significant differences in the conservation status of the biophysical units were found. Therefore vegetation composition is an important indicator of the conservation status; its definition helps to generate punctual strategies for conservation planning.