One of the large and increasingly important global problems is coastal eutrophication. Human disturbances includes large-scale fertilizer use which increases the nutrient availability in many coastal areas and can lead to toxic algal blooms or ecosystem turnover. Detecting past human disturbances in an area can improve the understanding of the nature and scope of the change induced and can be used in unraveling the differences between human induced change and natural variability. Charlotte Harbor (CH) is an until recently relatively undisturbed coastal-plain estuarine system in south-western Florida, U.S.A. Therefore, it is very useful in detecting anthropogenic and natural changes. A high-resolution multi-proxy study is conducted on a 210Pb dated sediment push core from CH, comprised of the last 140 years. Dinocyst and geochemical analyses provided consistent evidence for environmental changes induced by cultural eutrophication and human disturbance over the last 50 years. There is increased disturbance of the CH catchment and coastal area by deforestation (lower tree pollen, increased early succession species as Ambrosia), urbanization (population rise, large-scale waterfront development), pollution (waste water, P mining and slime spills) and agriculture (fertilizer usage, irrigation, water withdrawals). Changes in both biomarkers and palynology records suggests relative human-induced (cultural) eutrophication in the 1960s, which is increasingly evident since the 1980s AD. Dinocysts with aberrant cyst morphologies become dominant. These dinocysts, as ‘Spiniferites miratorii’, probably reflect lower salinity environments. As a result of human deforestation, population growth and urbanization activities, runoff and erosion increased in the CH area. This led to higher sedimentation rates, higher input of terrestrial OM and increased primary productivity due to higher nutrient inputs. Deforestation is visible in the pollen record from 1971 AD onwards. Nitrate levels of the Peace River rose exponentially around 1975 AD. Estuarine primary production of both diatoms (based on the highly branched isoprenoids (HBI) biomarker record) and of dinoflagellates (increased dinocyst flux) increased. It is thought that eutrophication and human disturbances make the estuary unstable and more sensitive for natural and anthropogenic changes. The more dynamic records from 1970s AD onwards indicate an increased sensitivity to salinity changes. It is possible that the increased variability reflects the natural climate oscillations as the Atlantic Multidecadal Oscillation (AMO) or the El Niño Southern Oscillation (ENSO).