The Clear Lake watershed, California, USA has been modified for agriculture since the arrival of Europeans in the early 1800s, and this has led to the deterioration of lake water quality. To assess the response of Clear Lake wetland sediments to recent environmental changes caused by watershed modification, physical and chemical properties of sediment cores at the inlet (Rodman Slough) and outlet (Anderson Marsh) were analyzed. ²¹⁰Pb dating showed increases of sedimentation rate for Anderson Marsh in the 1930s and 1980s, and those increases corresponded to algal blooms and the increase of P input into Clear Lake, respectively. Ranges of recent sedimentation and mass accumulation rates in Anderson Marsh were 0.41–0.52 cm/yr and 1070–1380 g m⁻² yr⁻¹. Accumulation rates of P, Ca, Mg, K, and Pb were slightly higher in Rodman Slough than in Anderson Marsh. Sediment analyses showed that the excess P originating from agricultural activities reach Clear Lake through Rodman Slough and were removed in the lake.