A high resolution sedimentary sequence recovered in the Tagus Prodelta has been studied in order to reconstruct paleoenvironmental conditions on the western Iberian Margin, Portugal, through the last ca. 2000 years, including the historical time when anthropogenic influence became significant. Benthic foraminiferal assemblages as well as stable isotopic composition of the benthic foraminifera Uvigerina sp. were investigated. Considerable environmental fluctuations are indicated by all these proxies. Between AD 400 and 1400 (1550–550 cal year BP), during a period including the Medieval Warm Period, bottom water temperatures, as reconstructed from Uvigerina sp., were high, 13.3 °C. In this time interval, species typical for shelf environments (Cassidulina laevigata, Nonion asterizans and Hyalinea balthica) maintained a high abundance along with opportunistic species like Bolivina dilatata and Bolivina pacifica, the most abundant species in the record. A faunal change occurred at around AD 1300–1400 (650–550 cal year BP), at the beginning of the Little Ice Age. After this, the environment became more variable in the Tagus Prodelta, as reflected by a decrease in faunal diversity and benthic foraminiferal composition and flux values. After about AD 1800 (150 cal year BP), bottom water temperatures rose to maximum values of the record. The disappearance of certain benthic taxa and the appearance of the species Saidovina karreriana indicate a change in bottom water conditions during the last 100 years, possibly induced by anthropogenic pollution.