Urban metabolism, a process of material, energy and water flows, consumption or transformation in the cities and outflows of wastes, has impacts on the shallow groundwater. This study addressed the relationship between the urban metabolic system and well water physicochemical and bacteriological quality in the coastal cities of Cotonou and Lomé. A participatory transdisciplinary approach, involving non-academics and academics stakeholders was used to analyse urban inflows and outflows related to groundwater quality. Standard methods were used to measure well water quality from 100 seasonal samples. Waste management revealed poor sanitation and hence a linear urban metabolism with no solid and liquid wastes and excreta recycling. This form of city metabolism reinforced by the seawater inflow is the main source of groundwater quality deterioration in Cotonou and Lomé. The principal water types Ca2+–Mg2+–Cl-– SO2-4？(48.21%), Na+–K+–Cl-–SO2-4 (65.9%) and the Gibbs diagram suggested water-rock interactions and dominance of cations exchange on the hydrogeological compositions, also seasonally controlled by saltwater intrusion or anthropogenic salinization. The water quality index on the range of 35.90 to 169.60 in Cotonou and 82.94 to 364.68 in Lomé indicated well water very poor quality to unsuitable for drinking. Moreover, the bacteriological quality was bad due to total coliforms (112 - 1812; 1 - 1000 UFC/100 mL respectively in Cotonou and Lomé), Escherichia coli (40 - 780; 1 - 112 UFC/100 mL), faecal enterococci/streptococcus (18 - 736; 1 - 118 UFC/100 mL). The findings could help to sustain groundwater quality by controlling the pollution sources linked to urban metabolism.
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