The Jurassic to Cretaceous strata exposed in the Rollrock Section, Sverdrup Basin, Arctic Canada, represent one of the northernmost continuous outcrops spanning this poorly understood transition. The Oxfordian–Valanginian mudstones of the Rollrock Section were deposited in a shallow marine environment and, as such, provide the ideal lithology to investigate the response of high latitude dinoflagellate cyst populations to the frequent environmental perturbations of this time. Using a multivariate statistical approach, distinct palaeoecologically significant groups are identified and directly linked to time and palaeoenvironments, allowing for the reconstruction of underlying long term palaeoenvironmental trends. These palaeoenvironmental trends are identified to be driven by sequence stratigraphic cycles. For the first time, fourth order sequences are recorded from this pivotal period in the Sverdrup Basin and reveal an additional level of short term climatic events that complicate the identification of long term trends. The relationship existing between marine phytoplankton and climate is utilised to decipher the interplay of long-term and short-term climate fluctuations, distinguishing them from evolutionary trends. Two groups of dinoflagellate cysts, identified by process morphology, are recorded to act as environmental proxies. High percentages of proximochorate dinoflagellate cysts, such as Trichodinium erinaceoides, indicate more proximal, high energy, nutrient rich conditions and are dominant in fourth order transgressive systems tracts. High percentages of chorate dinoflagellate cysts, such as Oligosphaeridium complex, signify distal, low energy, nutrient depleted conditions and are dominant in fourth order highstand systems tracts.