Along with environmental factors, agricultural activity is one of the main drivers of change in riparian landscapes of arid regions. Some agricultural practices are considered more sustainability-oriented than others. Despite this, their use is not widespread and their effect on the provision of ecosystem services is not clearly established. Thus, we propose an empirical framework for studying the effects of traditional agricultural practices on regulating ecosystem services in priority and spatially restricted ecosystems. Through spatial analysis and community field work, this study assesses changes in the use of two traditional agricultural practices: living fencerows and acequia irrigation systems and their effect on biodiversity and ecosystem service: habitat quality and carbon storage. Results show that the use of living fencerows promotes habitat quality and carbon storage, but their use is restricted by functional and socioeconomic factors. Acequia systems promote the provision of carbon storage but have a negative influence on habitat quality, and their use is changing mainly due to environmental and functional factors. The presence of obligate riparian vegetation in different configurations maintains the highest values for habitat quality and carbon storage, but it doesn’t provide the functional purpose of fencerows or acequias. We suggest that the expansion of voluntary and official conservation areas that promote regeneration of riparian vegetation adjacent and around agricultural areas could help mitigate floods, provide materials and suitable conditions for the maintenance of fencerows and acequias, enhance water and soil quality and many other services needed in agriculture. We consider our proposal to be useful for future assessments of ecosystem services tradeoffs and social-ecological dynamics in other understudied regions with predominantly agricultural activity.