Paleolimnological techniques were used to identify environmental changes in and around Lake Dudinghausen (northern Germany) over the past 4800 yr. Diatom-inferred total phosphorus (DI-TP) changes identify four phases of high nutrient levels (2600–2200 BC, 1050–700 BC, 500 BC–AD 100 and AD 1850–1970). During these high DI-TP phases, fossil pollen, sediment geochemistry and archaeological records indicate human activities in the lake catchment. Although the same paleo-indicators suggest increased human settlement and agriculture activity during the late Slavonic Age, the Medieval Time and the Modern Time (AD 1000–1850), DI-TP levels were low during this period. In the sediments, iron and total phosphorus were high from ∼AD 100 to 1850, likely due to increased inflow of iron-rich groundwater into the lake. Increased iron input would have lead to a simultaneous binding and precipitation of phosphate in the upper sediment and overlying water column. As a result, anthropogenic impact on Lake Dudinghausen was masked by these phosphorus-controlling processes from AD 1000 to 1850 and was not evident by means of DI-TP. In accordance with fossil pollen, sediment geochemistry and limited archaeological records, DI-TP levels were low from AD 100–1000. Groundwater levels likely rose during this period as the climate gradually changed toward colder and/or moister conditions. Such climate change likely led to reduced settlement activities and forest regeneration in the catchment area. Our results are concordant with similar studies from central Europe which indicate rapid decreasing settlement activities from AD 100 to 1000.