Groundwater-borne contaminants such as nutrients, dissolved organic carbon (DOC), coloured dissolved organic matter (CDOM) and pesticides can have an impact the biological quality of lakes. The sources of pollutants can, however, be difficult to identify due to high heterogeneity in groundwater flow patterns. This study presents a novel approach for fast hydrological surveys of small groundwater-fed lakes using multiple groundwater-borne tracers. Water samples were collected from the lake and temporary groundwater wells, installed every 50 m within a distance of 5–45 m to the shore, were analysed for tracer concentrations of CDOM, DOC, total dissolved nitrogen (TDN, groundwater only), total nitrogen (TN, lake only), total dissolved phosphorus (TDP, groundwater only), total phosphorus (TP, lake only), δ18O ∕ δ16O isotope ratios and fluorescent dissolved organic matter (FDOM) components derived from parallel factor analysis (PARAFAC). The isolation of groundwater recharge areas was based on δ18O measurements and areas with a high groundwater recharge rate were identified using a microbially influenced FDOM component. Groundwater discharge sites and the fractions of water delivered from the individual sites were isolated with the Community Assembly via Trait Selection model (CATS). The CATS model utilized tracer measurements of TDP, TDN, DOC and CDOM from the groundwater samples and related these to the tracer measurements of TN, TP, DOC and CDOM in the lake. A direct comparison between the lake and the inflowing groundwater was possible as degradation rates of the tracers in the lake were taken into account and related to a range of water retention times (WRTs) of the lake (0.25–3.5 years in 0.25-year increments). These estimations showed that WRTs above 2 years required a higher tracer concentration of inflowing water than found in any of the groundwater wells around the lake. From the estimations of inflowing tracer concentration, the CATS model isolated groundwater discharge sites located mainly in the eastern part of the lake with a single site in the southern part. Observations from the eastern part of the lake revealed an impermeable clay layer that promotes discharge during heavy precipitation events, which would otherwise be difficult to identify using traditional hydrological methods. In comparison to the lake concentrations, high tracer concentrations in the southern part showed that only a smaller fraction of water could originate from this area, thereby confirming the model results. A Euclidean cluster analysis of δ18O isotopes identified recharge sites corresponding to areas adjacent to drainage channels, and a cluster analysis of the microbially influenced FDOM component C4 further identified five sites that showed a tendency towards high groundwater recharge rate. In conclusion, it was found that this methodology can be applied to smaller lakes within a short time frame, providing useful information regarding the WRT of the lake and more importantly the groundwater recharge and discharge sites around the lake. Thus, it is a tool for specific management of the catchment.