Freshwater ecosystems are threatened by multiple anthropogenic stressors acting over different spatial and temporal scales, resulting in toxic algal blooms, reduced water quality and hypoxia. However, while catchment characteristics act as a ‘filter’ modifying lake response to disturbance, little is known of the relative importance of different drivers and possible differentiation in the response of upland remote lakes in comparison to lowland, impacted lakes. Moreover, many studies have focussed on single lakes rather than looking at responses across a set of individual, yet connected lake basins. Here we used sedimentary algal pigments as an index of changes in primary producer assemblages over the last ~200 years in a northern temperate watershed consisting of 11 upland and lowland lakes within the Lake District, United Kingdom, to test our hypotheses about landscape drivers. Specifically, we expected that the magnitude of change in phototrophic assemblages would be greatest in lowland rather than upland lakes due to more intensive human activities in the watersheds of the former (agriculture, urbanization). Regional parameters, such as climate dynamics, would be the predominant factors regulating lake primary producers in remote upland lakes and thus, synchronize the dynamic of primary producer assemblages in these basins. We found broad support for the hypotheses pertaining to lowland sites as wastewater treatment was the main predictor of changes to primary producer assemblages in lowland lakes. In contrast, upland headwaters responded weakly to variation in atmospheric temperature, and dynamics in primary producers across upland lakes were asynchronous. Collectively, these findings show that nutrient inputs from point sources overwhelm climatic controls of algae and nuisance cyanobacteria, but highlights that large-scale stressors do not always initiate coherent regional lake response. Furthermore, a lake's position in its landscape, its connectivity and proximity to point nutrients are important determinants of changes in production and composition of phototrophic assemblages.