Despite the increasing interest in climate change and water security, research linking climate change and groundwater quality is still at an early stage. This study explores the seasonal effect of the change in biogeochemical process for the redox-sensitive ions and metals Fe2+, Mn2+, SO42−, and NO3− to assess the groundwater quality of the shallow coastal aquifer of Eastern Dahomey Basin in southwestern Nigeria. Field physicochemical measurement of EC, pH TDS, Eh, salinity, temperature, and the static water level (SWL) was carried out on 250 shallow wells; 230 water samples were collected for analysis between June 2017 and April 2018. A spatial distribution map of these ions and metals showed an increasing concentration in the dry season water samples compared to those of the wet season. This higher concentration could be attributed to change in the intensity of hydrochemical processes such as evaporation, redox, and mineral precipitation. Results of linear regression modelling established significant relationships between SWL, SO42−, NO3−, Fe, and Eh for both wet and dry seasons with the p-value falling between 75% and 95%, which can also be seen in the plots of Eh/ORP against Fe2+, Mn2+, SO42−, and NO3−. These results revealed the influence of the redox process for both seasons, while also having a higher impact in the dry season while variation of concentration revealed decrease with increase in depth, which could be attributed to a decrease in well hydraulic properties and aeration. An Eh-pH geochemical diagram revealed NO3− as the controlling biogeochemical process over Fe in most of the sample wells. Concentrations of NO3−, Fe, and Mn are above the World Health Organization’s (WHO) standard for drinking water in most water samples. This study has established the link between climate change and groundwater quality in shallow coastal aquifers and suggested the need for strategic groundwater management policy and planning to ameliorate groundwater quality deterioration.