Providing historical data on riparian plant biodiversity and physico-chemical parameters of stream water in Mediterranean mountains helps to assess the effects of climate change and other human stressors on these sensitive and critical ecosystems. This database collects data from the main natural headwater streams of the Sierra Nevada (southeastern Spain), a high mountain (up to 3,479 meters above sea level, m.a.s.l.) recognized as a biodiversity super hotspot (Arroyo et al., 2022) in the Mediterranean Basin. On this mountain, rivers and landscapes depend on snowmelt water, representing an excellent scenario for evaluating global change's impacts. This dataset covers first- to third-order headwater streams at 41 sites from 832 to 1,997 m.a.s.l., collected from December 2006 to July 2007. Our goal is to supply information on the vegetation associated with streambanks, the essential physico-chemical parameters of stream water, and the physiographic features of the subwatersheds. Riparian vegetation data correspond to six plots sampled at each site, including total canopy, individual number, height and DBH (diameter at breast height) in woody species, and cover percentage for herbs. Physico-chemical parameters were measured in situ (electric conductivity, pH, dissolved O2 concentration, stream discharge) and determined in the laboratory [alkalinity, soluble reactive phosphate-phosphorus (SRP), total phosphorus (TP), nitrate-nitrogen (NO3-–N), ammonium-nitrogen (NH4+–N), total nitrogen (TN)]. Watershed physiographic variables comprise drainage area, minimum altitude, maximum altitude, mean slope, orientation, stream order, stream length, and land cover surface percentage. We recorded 197 plant taxa (67 species, 28 subspecies and 2 hybrids), representing 8.4% of the Sierra Nevada vascular flora. Due to the botanical nomenclature used, the database can be linked to FloraSNevada database (Lorite et al., 2020), contributing to Sierra Nevada (Spain) as a laboratory of global processes. For more information about the data, see the metadata document (Metadata_HeadwaterstreamSNevada.docx).