This datasets contains ecohydrological data collected for the research catchments at the Santa Rita Experimental Range (SRER, 31.817° N, -110.851° W) in southern of Arizona and the Jornada Experimental Range (JER, 32.585° N, -106.603° W) in southern New Mexico. The SRER catchment correspond to a mesquite savanna of the Sonoran Desert and the JER catchment is a mixed shrubland of the Chihuahuan Desert. Dataset includes the following ecohydrological variables at a daily scale: Year of measurement. Day of year (DOY) of measurement. Precipitation (P). Evapotranspiration (ET). Runoff (Q). Soil moisture (SM). Net Radiation (Rn). Sensible heat flux (H). Latent heat flux (λET). Gross primary production (GPP). Ecosystem respiration (Reco). Net ecosystem exchange (NEE). Air Temperature (Tair). Relative Humidity (RH). Vapour Pressure Deficit (VPD). Please cite the next data note together with the dataset: Vivoni, E. R., Perez-Ruiz, E. R., Keller, Z. T., Escoto, E. A., Templeton, R. C., Templeton, N. P., Anderson, C. A., Schreiner-McGraw, A. P., Mendez-Barroso, L. A., Robles-Morua, A., Scott, R. L., Archer, S. R., Peters, D. P. C. 2021. Long-term Research Catchments to Investigate Shrub Encroachment in the Sonoran and Chihuahuan Deserts: Santa Rita and Jornada Experimental Ranges. Hydrological Processes. 35: e14031. http://doi.org/10.1002/hyp.14031 This new version incudes three new variables (Tair, RH and VPD), and some carbon and water fluxes were updated to match data used in publications 1 and 2. Related publications: Perez-Ruiz, E.R., Vivoni, E.R., and Sala, O.E. 2022. Seasonal Carryover of Water and Effects on Carbon Dynamics in a Dryland Ecosystem. Ecosphere. 13(7): e4189. Vivoni, E.R., Perez-Ruiz, E.R., Scott, R.L., Naito, A.T., Archer, S.R., Biederman, J.A., and Templeton, N.P. 2022. A Micrometeorological Flux Perspective on Brush Management in a Shrub-encroached Sonoran Desert Grassland. Agricultural and Forest Meteorology. 313: 108763. Schreiner-McGraw, A.P., and Vivoni, E.R. 2018. On the Sensitivity of Hillslope Runoff and Channel Transmission Losses in Arid Piedmont Slopes. Water Resources Research. 54(7): 4498-4518. Schreiner-McGraw, A.P., and Vivoni, E.R. 2017. Percolation Observations in an Arid Piedmont Watershed and Linkages to Historical Conditions in the Chihuahuan Desert. Ecosphere. 8(11): e02000, http://dx.doi.org/10.1002/ecs2.2000 Anderson, C.A., and Vivoni, E.R. 2016. Impact of Land Surface States within the Flux Footprint on Daytime Land-Atmosphere Coupling in Two Semiarid Ecosystems of the Southwestern U.S. Water Resources Research. 52: 4785-4800. Schreiner-McGraw, A.P., Vivoni, E.R., Mascaro, G., and Franz, T.E. 2016. Closing the Water Balance with Cosmic-ray Soil Moisture Measurements and Assessing Their Relation with Evapotranspiration in Two Semiarid Watersheds. Hydrology and Earth System Sciences. 20: 329-345. Pierini, N.A., Vivoni, E.R., Robles-Morua, A., Scott, R.L., and Nearing, M.A. 2014. Using Observations and a Distributed Hydrologic Model to Explore Runoff Threshold Processes Linked with Mesquite Encroachment in the Sonoran Desert. Water Resources Research. 50(10): 8191–8215. Templeton, R.C., Vivoni, E.R., Méndez-Barroso, L.A., Pierini, N.A., Anderson, C.A., Rango, A., Laliberte, A.S., and Scott, R.L. 2014. High-Resolution Characterization of a Semiarid Watershed: Implications on Evapotranspiration Estimates. Journal of Hydrology. 509: 306-319. Vivoni, E.R., Rango, A., Anderson, C.A., Pierini, N.A., Schreiner-McGraw, A., Saripalli, S., and Laliberte, A.S. 2014. Ecohydrology with Unmanned Aerial Vehicles. Ecosphere. 5(10): art130. http://dx.doi.org/10.1890/ES14-00217.1