Abstract Long‐term biodiversity monitoring is crucial for freshwater ecosystems as it enables the detection of even subtle changes and biodiversity trends, guiding conservation efforts and ensuring the sustainability of these vital habitats. Despite becoming more commonly considered in the field of freshwater ecology and biological invasions, studies using long‐term time series from Türkiye's freshwater resources have remained scarce. To assess the availability of data and ultimately present a baseline for future efforts, we combined published museum records and samples from recent field studies from the highly anthropogenically‐altered Lake Bafa in Western Anatolia covering the period 1958–2019. Lake Bafa has a very diverse aquatic ecosystem, providing habitat for both freshwater and saltwater species, and is one of the allottees in Türkiye's inland fish production. In the current study, we investigated how fish populations in Lake Bafa were affected by environmental changes and examined changes in taxonomic and functional diversity of non‐native species over time. The analyses revealed—concomitant to an increase in native marine and freshwater species richness—an increase in non‐native species richness over time. Non‐native species did not interfere with native species' niche space, whereas applied models indicate that in this highly altered ecosystem, foremost temperature and salinity shaped the fish community over time, limiting the impacts of non‐native species. These results have implications for the fishery of the lake, which includes highly valuable catadromous fish species, highlighting the value and importance of collecting long‐term data in Türkiye to better understand both invasion dynamics and changes in the naturality of Turkish ecosystems. These findings further underline the importance of long‐term data to create new management strategies for the lake and to start restoration processes, thus improving fisheries management.