Groundwater quality is generally better than surface water quality but this is not sacrosanct because during recharge and abstraction, groundwater may be subjected to variations due to influence from natural and anthropogenic processes. The Togo and Dahomeyan aquifers are threatened by several anthropogenic activities like dumping of domestic and industrial wastes in open landfill sites. These activities can be sources of groundwater constituents and can pose adverse health effects on humans and the ecosystem but little is known about the hydrogeochemical characteristics of groundwater and its quality in the area. Therefore, the present study is aimed at unravelling the hydrogeochemical characteristics and quality of groundwater in the Togo and Dahomeyan aquifers in the Greater Accra Region of Ghana. A total of 37 groundwater samples were collected and analysed for the concentrations of major ions, minor ions, and trace elements. The results were used to compute water quality parameters like electrical conductivity, sodium adsorption ratio, sodium percent, and magnesium ratio to assess the quality of the water for irrigation purposes. Groundwater shows acidic to slightly alkaline pH and evolved from Mg–Na–HCO3, Ca–Na–Mg–HCO3, Na–Ca–Mg–HCO3–Cl to Na–Mg–Ca–HCO3 with other mixed water types, which reflect the local geology. Geochemical modelling indicates that groundwater is supersaturated with respect to goethite and hematite and saturated with respect to calcite, aragonite, and dolomite in some samples. Hydrochemical graphing and multivariate statistical analysis indicate that the chemistry of groundwater in the area is primarily controlled by an interplay of chemical weathering, mineral dissolution, ion exchange reactions, agricultural activities, and sewage disposal. The groundwater is not entirely suitable for drinking purposes because of high concentrations of EC, TDS, Na+, Cl−, F−, Fe, Mn, Pb, Cr, and Ni, which exceed their maximum permissible limits provided by the World Health Organization. The computed parameters for assessing the quality of the water for irrigation reveal that 64.9% of the samples are suitable for irrigation purposes. However, 35.1% of the samples show very high salinity and sodium hazard and thus, are unsuitable for irrigation purposes. Therefore, it is recommended that mixing of the high salinity and sodium water with low salinity and sodium water can improve crop yields.