• The lake is made up by mine groundwater and surface water and is in hydraulic balance. • The different sources of recharge at lake cause the meromixis in spite of little depth. • In winter the runoff inflow thickens mixolimnion and the system losses groundwater. • In summer the evaporation slims mixolimnion and the lake gains groundwater. • A conceptual model explaining its seasonal limnological evolution is advanced. The hydraulic system of the Concepción mine is made up of an open pit and an underground mine, which are currently flooded and hydraulically connected. The Concepción pit lake has shown permanent chemical stratification (meromictic lake), where two layers with different density and chemical composition can be differentiated: (i) a thick superficial layer of 11 ± 2 m deep, with a low concentration of dissolved solids (mixolimnion) and (ii) a thin bottom layer from 11 ± 2 m to 16 m deep (monimolimnion), exhibiting vertical changes in its physico-chemical parameters, with decreasing redox potential and increasing T, pH and dissolved solids content with depth. The distribution of the Concepción pit lake layers depends on recharge processes and the loss of water from the system. In winter, rainfall and runoff result in a rapid increase of lake levels. The lake regains its initial level whenever water is lost through an old mine adit, since galleries and shafts act as preferential pathways for inflowing and outflowing water. This network is connected to the bottom of the lake, resulting in the progressive downward movement of the chemocline. Furthermore, runoff generates a less dense superficial layer, which triggers the development of an ephemeral chemocline in the mixolimnion. In summer, the mixolimnion loses water by evaporation which is partially compensated by groundwater inflowing from the lake bottom, resulting in the upward movement of the permanent chemocline. During this period the water level in the system is below the outlet level, which therefore renders the outflow of water inactive. During this stage, the mixolimnion remains homogeneous and the shallow chemocline disappears. Taking into consideration the hydrochemical characteristics of this pit lake and the spatial distribution of the layers identified, a model that explains its seasonal limnological evolution is presented.