We evaluated changes in siliceous export production and the source of organic matter preserved in sediment core MD07-3109H recovered from the Gulf of Ancud, Chiloé Inner Sea (42°S, 72°W, water column depth: 328 m), southern Chile. We analyzed the abundance of siliceous microfossils (diatoms, silicoflagellates, sponge spicules, Chrysophyte cysts, phytoliths), geochemical proxies (weight percent silicon %SiOPAL, organic carbon, total nitrogen, C/N molar), and sediment stable isotopes (δ13Corg, δ15N). Chronology based on 210Pb and 14C provided an accumulated age of 144 years at the base of the core.Sediments of core MD07-3109H are predominantly marine in origin, averaging δ13Corg=–20.75‰±0.82, δ15N=8.7±0.35‰, and C/N=8.76±0.36. Marine diatoms compose 94% of the total assemblage of siliceous microfossils. Our record of productivity based on the mass accumulation rates of organic carbon, total nitrogen, SiOPAL, and total diatoms showed high values between 1863 and 1869 AD followed by a declining trend until 1921 AD, a transition period from 1921 to 1959 AD with fluctuating values, and a clear decreasing pattern from 1960 AD to the present. This marked reduction in productivity was associated with decreased precipitation and Puelo River streamflow (41°S), as well as a warmer and more stratified water column, especially since the 1980s.