This study aimed at characterizing groundwater evolution using hydrogeochemical facies and signatures in two basins with contrasting climate and geology, one in the central part and the other in the eastern coast of Tanzania. The Kimbiji (humid, unconsolidated) aquifer is covered by an unconfined layer in the upper parts and a confined layer in the lower parts, with strong artesian flow characteristics while groundwater in the Singida (semi-arid, consolidated) aquifer occurs in weathered shallow layers and in fractures of basement rocks. Fieldwork involved water sampling from precipitation, deep and shallow boreholes, springs and surface water from rivers and lakes in the two study areas. These were specifically conducted for hydrogeochemical analyses to unravel hydrogeochemical facies and signatures in the two aquifers. Physico-chemical water quality parameters [i.e., pH, electrical conductivity (EC) and total dissolved solids (TDS)] were measured in situ using HANNA HI 9829 Multiparameter Analyzer. Standard procedures for water sampling, preservation, transportation, and chemical analyses of major ions were conducted as documented in previous studies. Samples were carried and stored at 4 °C prior to their shipping and analyses at Water analysis and testing in environmental regions (WATER) laboratory in Iringa, Tanzania. The mechanism controlling groundwater geochemistry were revealed by assessing the reactions between groundwater and aquifer minerals. Chloro-Alkaline indices (CAIs) were used to study cation exchange processes between the groundwater and its host environment at stagnancy and/or during groundwater travel. The Gibbs ratio 1 values were found to range from 0.26 to 0.94 and Gibbs ratio 2 values ranged from 0.11 to 0.95. The majority of the samples irrespective of the contrast in climate and geology were observed to fall in the rock–water interaction zone. This is attributed to chemical weathering processes where the dissolution of rock forming minerals takes place. Some samples exhibited replacement of Na+ by Ca2+ or Mg2+ (S18), loss of Na+ through precipitation of evaporate rocks (S11, S13, S16, S19), and water flowing through crystalline rocks (S1, S2, S4, S6, S8, S10, S12, S13, S14, S21). The ratio Na+: Ca2+ > 1.0 (S1, S4, S8, S10, S12, S14, S17, S18, S19, S21) explains base ion exchange while the ratio < 1 implies a reverse ion exchange (S2, S6, S11, S13, S16).The Ca2+: SO42− + HCO3− ratio < 1.0 connotes groundwater flowing through a normal hydrological cycle (S1, S4, S8, S10, S12, S14, S17, S18, S2, S6, S11, S13, S21) and a ratio greater than 1 is an indication of Ca2+–Cl− brines (S16, S19). The HCO3−: Cl− hydrogeochemical signatures divided the Singida aquifer into upper water flow course, where groundwater recharge occurs (S52, S54, S56, S57, and S58) and the discharge zone, (S53, S59, S60, S61) which is a lower groundwater flow course. Interestingly, the Mg2+ + Ca2+: Na+ + K+ ratios as well confirmed that the Singida aquifer is a lower groundwater flow course (discharge zone). The greater than 1 Na+: Ca2+ ratios confirm the dominance of base ion exchange in the Singida aquifer as it has been explained by the CAIs and the Piper diagram. The Gibbs diagrams revealed that the hydrochemistry of groundwater in the Kimbiji and Singida aquifers are mainly in the rock weathering region, affirming that there is high dissolution with rock forming minerals. This is thus one of the main controls of groundwater mineralization in the two study areas. The similarity of hydrogeochemical signatures between a distant surface water body, Lake Inkhanoda and Mwankoko borehole in the Singida aquifer is an indication that there is a discernible interaction between groundwater and surface water, further revealing that the Singida aquifer is fed by sub-regional and regional groundwater flow systems.