<p>Nitrate pollution of freshwaters and methane emissions into the atmosphere are crucial factors in deteriorating the quality of drinking water and in contributing to global climate change. The nitrate dependent anaerobic methane oxidation and the anaerobic oxidation of ammonium (<i>anammox</i>) have the potential to reduce nitrogen loading of aquatic ecosystems and to reduce methane emissions to the atmosphere.</p> <p>Here, we report vertical concentration profiles and corresponding stable isotope compositions of CH<sub>4</sub>, NO<sub>3</sub><sup>−</sup>, NO<sub>2</sub><sup>−</sup> and NH<sub>4</sub><sup>+</sup> in the water column of a stratified lake, which suggest linkages between anaerobic oxidation of methane (AOM), denitrification, and <i>anammox</i>. In a water depth from 12 to 20 m, a methane-nitrate transition zone (NMTZ) was observed, where δ<sup>13</sup>C values of methane and δ<sup>15</sup>N and δ<sup>18</sup>O of dissolved nitrate markedly increased in concert with decreasing concentrations of methane and nitrate. These data patterns, together with a simple 1D diffusion model show that the non-linear methane concentration profile cannot be explained by diffusion or micro-aerobic methane oxidation, and that microbial oxidation of methane coupled with denitrification under anaerobic conditions is the most likely explanation for these data trends.</p> <p>In the methane zone at the bottom of the NMTZ (20 m to 22 m) δ<sup>15</sup>N of ammonium increased by 4 ‰, while ammonium concentrations decreased. In addition, a strong <sup>15</sup>N enrichment of dissolved nitrate was observed at a water depth of 20 m, suggesting that <i>anammox</i> is occuring together with denitrification coupled to AOM. The conversion of nitrite to N<sub>2</sub> and nitrate during <i>anammox</i> is namely associated with an inverse N isotope fractionation and may explain the observed increasing offset (Δδ<sup>15</sup>N) of 26 ‰ between δ<sup>15</sup>N values of dissolved nitrate and nitrite at a water depth of 20 m compared to the Δδ<sup>15</sup>N<sub>nitrate-nitrite</sub> of 11 ‰ obtained in the NMTZ between a water depth of 16 m and 18 m.</p> <p>The geochemcical zones were found to contain significantly different microbial communities that consist of bacteria known to be involved in denitrification with AOM (<i>Crenothrix</i> and NC10), and <i>anammox</i> (<q><i>Candidatus</i> Anammoximicrobium</q>), confirming the presence of microbial groups potentially responsible for the proposed linkages between AOM, denitrification, and anammox. This study gives insights into the yet overlooked AOM-denitrification-anammox process in stratified lakes that can regulate methane emisssions from and nitrogen concentrations in lakes.</p>