Saline wetlands represent potential natural analogs for reclaimed wetlands in the Athabasca Oil Sands Region (AOSR). Thus, an understanding of the drivers of salinity changes in natural wetlands can provide insight into how reconstructed peatlands in the AOSR may evolve given that they are constructed with saline oil sands reclamation materials. Here, we investigate the nature of salinity changes from the analysis of sediment cores at three ponds situated within a saline peat-forming wetland near Fort McMurray (Alberta). Past changes in salinity were reconstructed using weighted-averaging transfer functions based on diatoms and an environmental dataset from 32 saline boreal ponds. Results reveal complex “precipitation—surface water—groundwater” interactions associated with differences in the hydrologic functioning of the studied ponds, and their connectivity with shallow groundwater aquifers and adjacent wetlands. Relationships between cumulative departure from mean precipitation and DI-salinity suggest that precipitation may control salinity both directly and indirectly. In ponds recharged predominantly by meteoric water, precipitation may govern salinity directly by dilution of salt content in water, so that rises in precipitation result in a salinity decline. In ponds situated within a saline groundwater discharge zone, salinity may be influenced by precipitation indirectly through recharge of the saline aquifer, so increases in precipitation lead to rises in salinity. Our study suggests that complex salinity response to precipitation change, coupled with notable range of salinity fluctuation within natural saline fens should be considered while designing saline constructed wetlands and predicting their potential resilience under climate change.