<p>Agricultural activities are the leading cause of the eutrophication of waterbodies downstream of farmed lands. Nature-based water protection measures, such as treatment wetlands (TW), are highly effective in reducing diffuse agricultural pollution; however, most studies evaluate their performance over short monitoring periods, potentially overlooking long-term ecological development and interannual variability. This study presents a long-term (7-year period) overview of a well-established in-stream free-water surface (FWS) TW to reduce diffuse agricultural pollution in a temperate climate zone in southern Estonia. The TW consists of two sequential in-stream FWS TWs with a catchment area of 2.2 km². The TWs are mainly vegetated with cattail (<i>Typha latifolia</i>) and common reed (<i>Phragmites australis</i>). Biweekly monitoring of water parameters was conducted from 2017 to 2023. The results for the entire study period show positively trending removal efficiency with high seasonal variability in both wetlands for total nitrogen, total phosphorus, and total organic carbon, with retention rates reaching up to 11.33, 0.64, and 17.05 kg ha⁻¹ d⁻¹, respectively. The observed increase in treatment efficiency coincided with vegetation maturation and ecosystem development, showing clearly that wetland performance evolves substantially over time. Near full vegetation cover was achieved after 7 years in both wetlands. This long-term dataset provides rare observation into the temporal dynamics, maturation processes, and resilience of in-stream FWS TWs under temperate climatic conditions and demonstrates the need for multi-year continuous monitoring for assessing their treatment capacity and guiding design and management strategies.</p>