We examined late Holocene (ca. 3300 yr BP to present-day) climate variability in the central Northwest Territories (Canadian Subarctic) using a diatom and sedimentological record from Danny's Lake (63.48ºN, 112.54ºW), located 40 km southwest of the modern-day treeline. High-resolution sampling paired with a robust age model (25 radiocarbon dates) allowed for the examination of both lake hydroecological conditions (30-year intervals; diatoms) and sedimentological changes in the watershed (12-year intervals; grain size records) over the late Holocene. Time series analysis of key lake ecological indicators (diatom species Aulacoseira alpigena, Pseudostaurosira brevistriata and Achnanthidium minutissimum) and sedimentological parameters, reflective of catchment processes (coarse silt fraction), suggests significant intermittent variations in turbidity, pH and light penetration within the lake basin. In the diatom record, we observed discontinuous periodicities in the range of ca. 69, 88-100, 115-132, 141-188, 562, 750 and 900 years (>90% and >95% confidence intervals), whereas the coarse silt fraction was characterized by periodicities in the >901 and <61-year range (>95% confidence interval). Periodicities in the proxy data from the Danny's Lake sediment core align with changes in total solar irradiance over the past ca. 3300 yr BP and we hypothesize a link to the Suess Cycle, Gleissberg Cycle and Pacific Decadal Oscillation via occasional inland propagation of shifting air masses over the Pacific Ocean. This research represents an important baseline study of the underlying causes of climate variability in the Canadian Subarctic and provides details on the long-term climate variability that has persisted in this region through the past three thousand years.