We present reconstructions of late Holocene changes in the source of organic matter and siliceous export production in the Relocanví Fjord (41°S, 72°W), Northern Chilean Patagonia, based on organic carbon content, δ¹³C_org, N/C ratio, diatom assemblages and biogenic silica contents from three sediment cores. The age models are based on a combination of ²¹⁰Pb profiles, AMS ¹⁴C dating, and on the first occurrence of the diatom Rhizosolenia setigera f. pungens, as a stratigraphic marker in the fjords. The cores span the last 300 to 700 yr. Diatoms dominate the siliceous assemblages in the three cores (98% on average). Our results suggest that precipitation seasonality in the region of Reloncaví was high in CE 1300–1400 and CE 1700–1850, with a clear decreasing trend since CE 1850. The latter trend is in agreement with instrumental records and tree-ring reconstructions. These fluctuations seem to be associated with the Southern Annular Mode (SAM).