An assessment of storage changes within the Cretaceous sandstones of Lokoja Formation constituting the sedimentary part of Lokoja and its environs was carried out using USGS GSFLOW-1.0 software to investigate reasons for water problems such as drying of streams and failure of wells commonly experienced in the area. Daily meteorological data from year 2001 to 2010 and hydraulic conductivity for the area were used as input for the model simulation. Model results indicate that storage in the watershed takes place in the soil-zone, unsaturated-zone and saturated-zone and that storage takes place at different periods in the storage zones. Three storage cycles were identified in each of the storage zones. Soil-zone storage is generally higher during the second and third cycles. Storage in the unsaturated zone is lowest in the first cycle with thickness of the zone decreasing to minimum in the second cycle as storage increases to maximum. Storage increased to maximum in the second cycle of the saturated zone with the first and third cycles showing negative storage changes as unsaturated zone thickness increased. Surface runoff, interflow, and groundwater discharge in form of springs contribute stream flow to the watershed. Failure of wells in the area is attributed to the geology and water loss to the surface leading to insufficient water reaching the saturated zone for storage.