Lagoons are important ecosystems occupying large coastal areas worldwide. Lagoons contain various mixtures of marine and freshwater sources which are highly dynamic in time. However, it often remains a challenge to identify and quantify dynamic changes of water sources, particularly in heterogeneous lagoon systems like the Koycegiz-Dalyan lagoon (KDL), which is located at the south-west of Turkey on the Mediterranean Sea coast. The objective of this study was to quantify different contributions of potential water sources i.e. surface water, groundwater and seawater in the lagoon and how these water sources changed over time and space. In the wet-and dry-season stable isotopes of water, chloride concentration (Cl-) and salinity were measured in two depths in the lagoon and surrounding water bodies (sea, lake, groundwater). Different components of water sources were quantified with a three component endmember mixing analysis. Differences in Cl- and stable isotopes over time indicated the dynamic behaviour of the system. Generally, none of the groundwater samples was impacted by water of the Mediterranean Sea. During the wet season, most of the lagoon water (> 95 %) was influenced by freshwater and vertically well mixed. During the dry season, high Cl- in the deeper sampling locations indicated a high contribution of marine water throughout the entire lagoon system due to saltwater intrusion. However, a distinct layering in the lagoon was obvious from low Cl- and depleted isotope contents close to the surface supporting freshwater inflow into the system even during the dry season. Besides temporal dynamics also spatial heterogeneities were identified. Changes in water sources were most evident in the main lagoon channel compared to more isolate lagoon lakes, which were influenced by marine water even in the wet season, and compared to side branches indicating slower turnover times. We found that environmental tracers helped to quantify highly dynamic and heterogeneous contributions of different water sources in the Koycegiz-Dalyan lagoon.