Knowledge of groundwater flow, and accordingly, groundwater residence time is immensely important for the sustainable management of groundwater resources. This requires a good conceptual model of the aquifer system. In this paper, a conceptual model based on the interpretations of hydrogeological and hydrochemical data, as well as measurements of environmental tracers (18O, 2H, 3H) was formulated for a semiconfined aquifer system in Eastern Slavonia in Croatia. The aquifer system is composed of Quaternary gravel and sand and silty–clayey interlayers and is covered with low permeability deposits. Measurements of water levels and environmental tracers in the study area clarified the groundwater flow evolution from the recharge area to the discharge area. The content of stable isotopes confirmed that the groundwater originates from precipitation. The tritium content and geochemical processes (such as cation exchange, silicate weathering) suggested a relatively long residence time of groundwater in the part of the aquifer system that is further from the Sava River. The same is confirmed by the results of calculated particle tracking pathlines. •Recharge mechanism and groundwater flow evolution were studied.•Hydrogeological, hydrochemical and isotopic methods were combined successfully and used to improve conceptual model.•The results confirmed recharge by rainfall infiltration as the main source of water.•Groundwater residence time of several decades was confirmed by associated methods.