A 5-day detailed field investigation at a new RBF test well gallery in Embaba, Cairo, was conducted to evaluate the hydraulic setting and the behavior of iron and manganese. The well gallery consists of six vertical wells placed along a straight line parallel to the Nile riverbank. A low anisotropy factor for the aquifer (k_f,h:k_f,v) of 1.7 was determined by evaluation of a multistep pumping test. Travel times between 11 days from the river toward the central wells and 22 days toward the outermost wells were estimated by groundwater flow modeling and particle tracking. The riverbed is rich in fine suspended sediments that have elevated iron and nitrogen concentrations. Depth-dependent water sampling during regular well operation indicates that the thick organic-, Fe- and Mn-rich riverbed is the primary source for ammonium, iron and manganese in the bank filtrate. Iron-rich groundwater flow from the opposite riverbank was identified as a secondary source of iron in the pumped water. The vertical position of the filter screen affects total travel times but would not reduce the portion of Mn-rich bank filtrate. The authors recommend continuous well operation for achieving stable water quality and lowering the risk of well clogging.