The La‐Lantejuela playa‐lakes endorheic complex is a groundwater‐dependent ecosystem located within the Guadalquivir River Basin (Southern Spain) in an area mainly devoted to agriculture production with increasing groundwater extractions for irrigation from the Osuna‐La Lantejuela (O‐LL) aquifer. The O‐LL aquifer was hydrogeologically characterised in previous works made by the authors. New data and the combination of more field observations, together with the use of morphologic indexes of the playa lakes, has permitted to analyse the relationships between the aquifer and each one of the playa lakes in the complex, assessing whether their hydrological functioning would have been affected by the expansion of irrigated agriculture. Furthermore, the analysis of the results obtained has allowed establishing a hypothesis of the hydrological functioning of the whole system under natural conditions. This case study represents a useful example to understand how agriculture in semi‐arid environments can induce alterations on the wetlands hydrological functioning.