Background: The microbiological quality of three vegetable crops (cabbages, carrots, lettuces) and their irrigation water from the lake system of the city of Yamoussoukro were studied. The pollution indicator used is Escherichia coli (E. coli), of the thermotolerant coliform family. Methods: During the period 2017-2019, in four dry and four wet seasons, a total of 744 water samples and 13392 vegetable samples were collected in five (5) lakes belonging to the lake system. The lakes were selected because of their position in the system. The E. coli loads were evaluated after isolation on a specific COMPASS ECC Agar and confirmed with Polymerase chain reaction (PCR) and the physicochemical parameters of the lakes, evaluated according to their respective ISO standards. Result: In irrigation waters, bacterial loads and physico-chemical parameters generally have evolved from the upstream lakes to those downstream of the lake system (from lake A to lake E). Values were higher during the rainy seasons. E. coli loads on vegetables were strongly correlated with those of irrigation water, especially in dry seasons. Spearman's correlations revealed significant correlations between turbidity, DOC and bacterial loads. The risk of bacterial transmission between lake waters and surrounding vegetables is proven.