The flooding of unprofitable underground mines is one of the methods of their closure. After the drainage of the mine has stopped, the voids left in the rock mass as a result of mining, are filled with inflowing groundwater. In this way, reservoirs of groundwater with specific physicochemical parameters are formed. These parameters depend on the interaction of the water flowing into the workings with the rock formations. It was the economic situation in the 1990s that led to the closure of hard coal mines in the Nowa Ruda Coal Basin, where the flooded “Nowy I” shaft is located. In that shaft, in 2008, hydrogeological research was performed and groundwater samples from five various depths were collected. The aim of the study was to recognize if groundwater stratification occurs in the shaft. In 2015, a sample of the water outflowing through the “Aleksander” adit was taken to check the potential influence of mine flooding on the environment and to confirm the changes in groundwater chemistry over time. These were the first, and so far, the only studies on the chemical composition of water in the flooded mine in that area. The article presents results of the preliminary research, which confirmed the existence of not obvious hydrogeochemical stratification in the shaft. It can be assumed that below the depth of 350 m, the water circulating through mining excavations exhibits the highest electrical conductivity and the highest concentration of Ca2+, K+, SO42−, Fetot. In the depth range of 320–380 m there is a transition zone, in which a decrease of Eh value and a change of reduction and oxidation is recorded. Above this zone, infiltration water inflow, from outside the shaft casing, dominates. The research shows that it would be necessary to perform additional sampling of the water in the shaft at greater depths, as well as to perform isotope analysis and periodical tests for at least several years. This would allow for a more complete characterisation of hydrogeochemical processes taking place in the flooded mine.