Ponds and lakes distributed across northern treeline in the Hudson Bay Lowlands near Churchill (Manitoba) were revisited to analyse and document the local ecoclimatic and limnological changes that occurred over the period 1997-2012. Our analyses revealed that single events may cause significant changes in salinity, pH and silicate content because of the limited buffer capacity of the inter-connected waters. Planktic freshwater microcrustaceans (Cladocera) presented less diverse assemblages and appeared to favour waters that are situated in the boreal forest, while the diversity of benthic species assemblages (Cladocera and Ostracoda) was highest in waters located closer to the coastline and in open tundra vegetation. We identified three species that are distinctive for the boreal ecozone (i.e., Candona acuta, Can. acutula and Can. decora) and two species (i.e., Tonnacypris glacialis and Can. rawsoni) that are elements of (sub-)arctic landscapes and potentially endangered as the northern treeline expands due to rapid warming. These species are thought to be useful indicators for future ecosystem quality assessments and/or ecosystem service management programs. Our findings were compared to other studies completed in the boreal Yukon Territory and revealed that species diversity is closely linked to landscape history.