We investigated the depositional trends of total particles, carbon and nitrogen in a newly created, 600-km2 hydroelectric reservoir in Northern Québec, and compared the results with those observed in lakes of the surrounding region. We show that particulate fluxes exhibit a large degree of spatial heterogeneity in both the reservoir (68–548 mg POC m−2 d−1 and 5–33 mg PN m−2 d−1) and the natural lakes (30–150 mg POC m−2 d−1 and 3–12 mg PN m−2 d−1) and that on average, settling fluxes of the reservoir (211 ± 46 mg POC m−2 d−1 and 14 ± 3 mg PN m−2 d−1) exceeded lake deposition (79 ± 13 mg POC m−2 d−1 and 7 ± 1 mg PN m−2 d−1) by approximately two-fold. Our results also show that the nature of the organic matter reaching the sediments was significantly different between lakes and the reservoir, which can have consequences for benthic metabolism and the long-term storage. We found that sinking fluxes in the reservoir were mostly regulated by local morphological and hydrological conditions, with higher fluxes along or in the vicinity of the old riverbed (average 400 ± 73 mg POC m−2 d−1 and 24 ± 5 mg PN m−2 d−1) and lower fluxes in calmer zones such as side bays (average 106 ± 10 mg POC m−2 d−1 and 8 ± 1 mg PN m−2 d−1). In lakes, where settling fluxes were not linked to the trophy, or dissolved organic carbon, the actual nature of the sedimenting organic material was influenced by lake morphometry and the relative contribution of algal versus terrestrial sources. We conclude that re-suspension and erosion play a major role in shaping the reservoir sinking fluxes which explain both, the higher reservoir deposition and also some of the qualitative differences between the two systems. Despite all these differences, sinking particulate organic carbon fluxes were small and surprisingly similar relative to the surface carbon dioxide emissions in both the reservoir and lakes, representing approximately 16–17 % of the carbon efflux estimated for these same systems in 2008.