The climate system in the North Atlantic region is complex and influenced by outside forcings as well as internal modes of the system. Modeling and observational work have suggested that a better understanding of the connections between ocean- and atmosphere-driven variability could lead to predictive power for North American and European weather patterns. Here we present a new millennial-length proxy record of estuarine fossil pigments and use it to investigate cyclic components of North Atlantic climate through the effects on estuarine ecosystems. The time series exhibits significant cyclic components that can be related to two of the dominant internal modes of climate variability in the region: the North Atlantic Oscillation (NAO) and the Atlantic Multidecadal Oscillation (AMO). The NAO signal is associated with internal atmospheric variability, while the AMO has been linked to previously modeled and observed changes in thermohaline circulation and meridional heatflux. In our record, the dominant periodicity of the AMO has shifted over time, in concert with Medieval Warm Period–Little Ice Age–Present Warm Period transitions. A relationship between an intermittent NAO cycle and the AMO signal suggests coupling of the ocean-atmosphere system at multidecadal time scales. Although the causal relationship is not resolved, predictive models of Northern Hemisphere interannual weather patterns and estuarine productivity may be improved by incorporating the results of this study.