Transformation or modification of vegetation distribution and structure in arid riparian ecosystems can lead to the loss of ecological function. Mexico has 101,500,000 ha of arid lands, however there is a general lack of information regarding how arid riparian ecosystems are being modified. To assess these modifications, we use eight sites in the San Miguel River (central Sonora) to analyze (1) riparian vegetation composition, structure and distribution using field sampling and remote sensing data from Unmanned Aerial Vehicles (UAV); (2) productivity (proxies), using vegetation indices derived from satellite data; and (3) variability posed by riparian vegetation and vegetation adjacent to riparian habitats. The development of a simple yet informative Anthropogenic-disturbance Index (ADI) allowed us to classify and describe each study site. We found sharp differences in vegetation composition and structure between sites due to the absence/presence of obligate-riparian species. We also report significant difference between EVI (Enhanced Vegetation Index) values for the dry season among vegetation types that develop near the edges of the river but differ in composition, suggesting that land cover changes form obligate-riparian to facultative-riparian species can lead to a loss in potential productivity. Finally, our tests suggest that sites with higher disturbance present lower photosynthetic activity.