The data is related to the paper of "The effect of river flow and groundwater variations on hyporheic zone characteristics in alternate bars" published by Monofy and Fulvio (2019) in the journal of water resources research (wrr). The study is based on a numerical model of hyporheic flow in a built synthetic river reach with imposed alternate bars geometery. Five river flow discharges are investigated, and under each discharge values, three groundwater flow conditions are examinated; netural condition, where there is no groundwater flux on the bottom of the domain; losing condition, where the groundwater domain is losing flow thourgh its bottom (to an imaginary aquifer); gaining condition, where the groundwater domain is gaining flow through its bottom (from an imaginary aquifer). In case of gaining and losing conditions different values of groundwater are tried creating different simulations for each specific river flow and groundwater condition (in total 43 simulations). The data are organized as following; five major files represent five river flows, in each file there are three submajor files represent three groundwater conditions (netural, gaining and losing). Inside neutral files, the data obtained from the surface water modeling as well as groundwater modeling and particle tracking are provided in .csv files. while for losing and gaining conditions, the files are subdivided based on the value of imposed groundwater flow. The .csv files contain the pressure heads on streambed, negative fluxes into the streambed, positive fluxes out of the streambed which can be used to map the overall flux distribution through the bed, and finally the results of particles tracking, in which each pathline of the hyporheic flux is defined with its associated characteristics, as residence time, maximum depth, hyporheic flux ...etc.