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Lakes play an important role in catchment carbon (C) balances. However, the role of lakes in landscape C cycling in changing climate is highly uncertain. We studied C pools in a chain of five boreal lakes and compared the C fluxes during a wet and a dry year. The included pools were dissolved inorganic carbon (DIC) and total organic carbon (TOC) in lake water, as well as C pools in littoral macrophytes and lake sediments. The estimated C fluxes consisted of hydrological input and output of DIC and TOC, emission of carbon dioxide (CO2) to the atmosphere, DIC incorporated as organic carbon in primary production of phytoplankton and littoral macrophytes, and sedimentation of C. The riverine input of C into the lakes increased remarkably (40–210%) in the year with high precipitation. Simultaneously, there was a clear increase in the flux of CO2 to the atmosphere from the three small uppermost lakes, whereas in two large lowland lakes the CO2 fluxes were higher during the warm dry year. On the landscape scale, the role of small lakes (area <1 km2) was emphasized in net C accumulation, whereas the large lowland lakes released more CO2 to the atmosphere. In parallel, the concentration of TOC in the water column decreased downstream the lake chain whereas DIC increased. The largest pool of C (>98%) in all the lakes was in the sediment. Sediment C store, calculated relative to the lake area, was positively correlated with lake water TOC (r2 = 0.93, P < 0.05) and Fe (r2 = 0.96, P < 0.05) concentrations. Lake water Fe content was also a good predictor for the long‐term accumulation (r2 = 0.99, P < 0.01), as well as gross sedimentation rate of organic carbon (r2 = 0.48, P < 0.01).

Methane efflux was studied in stands of three emergent macrophyte species (Equisetum fluviatile, Schoenoplectus lacustris and Phragmites australis) commonly found in the littoral zone of boreal lakes. In vegetation stands with relatively low methane (CH 4 ) emissions (o0.3 mol m À2 (ice-free period) À1 ), the seasonal variation of CH 4 efflux was better correlated with the dynamics of plant growth than variation in sediment temperature. In dense and productive vegetation stands that released high amounts of CH 4 (2.3-7.7 mol m À2 (ice-free period) À1 ), the seasonal variation in CH 4 efflux was correlated with sediment temperature, indicating that methanogens were more limited by temperature than substrate supply. The bottom type at the growth site of the emergent plants significantly influenced the ratio of CH 4 efflux to aboveground biomass of plants (Eff : B). The lowest Eff : B ratio was found in E. fluviatile stands growing on sand bottom under experimental conditions and the highest in P. australis-dominated littoral areas accumulating detritus from external sources. The future changes expected in the hydrology of boreal lakes and rivers because of climatic warming may impact the growth conditions of aquatic macrophytes as well as decomposition and accumulation of detritus and, thus, CH 4 effluxes from boreal lakes.

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Summary 1. Spatial variation of methane (CH4) efflux from the littoral zone of a meso‐eutrophic boreal lake was studied with a closed‐chamber technique for three summer days in 22 vegetation stands, consisting of three emergent and three floating‐leaved species. 2. Between‐species differences in CH4 emission were significant. The highest emissions were measured from the emergent Phragmites australis stands (0.5–1.7 mmol m−2 h−1), followed by Schoenoplectus lacustris > Equisetum fluviatile > Nuphar lutea > Sparganium gramineum > Potamogeton natans. Within‐species differences between stands were not significant. 3. In P. australis stands, the stand‐specific mean CH4 emission was significantly correlated with solar radiation, probably indicating the role of effective pressurised ventilation on CH4 fluxes. The proportion of net primary production emitted as CH4 was significantly higher in P. australis stands (7.4%) than in stands of S. lacustris and E. fluviatile (both 0.5%). 4. In N. lutea stands, CH4 efflux was negatively correlated with the mean fetch and positively with the percentage cover of leaves on the water surface. There were no differences in CH4 efflux between intact N. lutea leaves and those grazed by coleopteran Galerucella nymphaeae. In S. graminaeum and P. natans stands, CH4 effluxes were not related to any of the measured environmental variables. 5. For all vegetation stands, the biomass above water level explained about 60% of the observed spatial variation in CH4 emission, indicating the important role of plants as gas conduits and producers of substrates for methanogens in the anoxic sediment.