The Upper San Pedro River is one of the few remaining undammed rivers that maintain a vibrant riparian ecosystem in the southwest United States. However, its riparian forest is threatened by diminishing groundwater and surface water inputs, due to either changes in watershed characteristics such as changes in riparian and upland vegetation, or human activities such as regional groundwater pumping. We used satellite vegetation indices to quantify the green leaf density of the groundwater-dependent riparian forest from 1984 to 2012. The river was divided into a southern, upstream (mainly perennial flow) reach and a northern, downstream (mainly intermittent and ephemeral flow) reach. Pre-monsoon (June) Landsat normalized difference vegetation index (NDVI) values showed a 20% drop for the northern reach (P < 0·001) and no net change for the southern reach (P > 0·05). NDVI and enhanced vegetation index values were positively correlated (P < 0·05) with river flows, which decreased over the study period in the northern reach, and negatively correlated (P < 0·05) with air temperatures in both reaches, which have increased by 1·4 °C from 1932 to 2012. NDVI in the uplands around the river did not increase from 1984 to 2012, suggesting that increased evapotranspiration in the uplands was not a factor in reducing river flows. Climate change, regional groundwater pumping, changes in the intensity of monsoon rain events and lack of overbank flooding are feasible explanations for deterioration of the riparian forest in the northern reach.