A holistic understanding of the chemical recovery of lakes from arsenic (As) pollution requires consideration of within-lake biogeochemical cycling of As and processes occurring in the surrounding catchment. This study used a watershed mass balance approach, complemented by experimental sediment incubations, to assess the mobility and transport of As within a subarctic watershed (155 km2) impacted by more than 60 years of atmospheric mining emissions. The period of record spanned a transition from drought to high streamflow between September 2017 and September 2019, which yielded insights into the interacting effects of hydrology and within-lake biogeochemical cycling of As. Internal loading of As from contaminated lake sediments (25–46 kg As year−1) and contributions from terrestrial sources (16–56 kg As yr−1) continue to negatively impact lake water quality (19–144 μg As L−1), but the relative importance of these loads varies seasonally and inter-annually in response to changing hydrological conditions. Wet conditions resulted in greater transport of As from terrestrial reservoirs and upstream areas, shorter lake water retention time, and increased the downstream export of As. During dry periods, the lake was disconnected from the surrounding watershed resulting in limited terrestrial contributions and longer lake water residence time, which delayed recovery due to the greater relative influence of internal loading from contaminated sediments. This study highlights that changing hydroclimatic regimes will alter trajectories of chemical recovery for arsenic impacted lakes through the coupling of within-lake and watershed transport processes.