The forearc of the convergent margin offshore Costa Rica is a region characterized by strong advection of methane-charged fluids causing the formation of ubiquitous cold seeps (mounds). Presented here are the first measurements of microbial anaerobic oxidation of methane (AOM) and sulfate reduction (SR) rates in sediments from two mounds (11 and 12), applying radiotracer techniques in combination with numerical modelling. In addition, analysis of microbial, methane-dependent carbonate δ<sup>18</sup>O, δ<sup>13</sup>C, and <sup>87</sup>Sr / <sup>86</sup>Sr signatures constrained the origin of the carbonate-precipitating fluid. Average rates of microbial activities differed by a factor of ~5 to 6 between Mound 11 (AOM 140.71 (±40.84 SD) mmol m<sup>−2</sup> d<sup>−1</sup>, SR 117.25 (±82.06 SD) mmol m<sup>−2</sup> d<sup>−1</sup>) and Mound 12 (AOM 22.37 (±0.85 SD) mmol m<sup>−2</sup> d<sup>−1</sup>, SR 23.99 (±5.79 SD) mmol m<sup>−2</sup> d<sup>−1</sup>). Modelling results yielded upward fluid advection velocities of 200 cm yr<sup>−1</sup> at Mound 11 and 15 cm yr<sup>−1</sup> at Mound 12. Analysis of oxygen and carbon isotope variations of authigenic carbonates from the two locations revealed more enriched values for Mound 11 (δ<sup>18</sup>O : 3.18 to 6.15‰; δ<sup>13</sup>C: −14.14 to −29.56‰) compared to Mound 12 (δ<sup>18</sup>O : 3.09 to 4.48‰; δ<sup>13</sup>C : −39.53 to −48.98‰). The variation of carbonate <sup>87</sup>Sr / <sup>86</sup>Sr indicated considerable admixture of deep-source fluid at Mound 11, while seawater <sup>87</sup>Sr / <sup>86</sup>Sr characteristics prevailed at Mound 12 during precipitation. The present study is in accordance with previous work supporting considerable differences of methane flux between the two mounds. It also strengthens the hypothesis of a dominant deep fluid source with thermogenic methane at Mound 11 versus a shallow source of biogenic methane at Mound 12. The results demonstrate that measurements of methane-driven microbial activity in combination with numerical modelling are a valid tool for constraining recent methane fluxes in the study area. In addition, the analysis of methane-derived authigenic carbonates provides an independent line of evidence for long-term fluid contribution to the porewater chemistry of shallow sediments in the study area.