Abstract Although the transfer of methane‐derived carbon (MDC) to benthic macroinvertebrates such as chironomid larvae and oligochaetes has been well documented, knowledge of the transfer of MDC to fish is limited. We investigated the MDC contribution to 28 fish species through their growth stages and examined the relationship between fish traits including body size, and MDC contribution to fish within species in Lake Kasumigaura, Japan. We used carbon stable isotope ratios and a two‐source mixing model (methane‐oxidation bacteria [MOB] and particulate organic matter) to estimate the MDC contribution to fish. The MDC contribution to individual fish ranged from 0% to 21.5%. Anguilla japonica showed the highest MDC contribution (mean 3.8%). Fish species were classified into four groups according to two criteria: (a) whether the correlation between the MDC contribution and fish size (within species) was significantly negative (negative vs. not significant; ns); and (b) whether the 90th percentile of MDC contribution was 0% or not. The mean MDC contribution was highest (2.18% ± 2.93%, 12 species) for the group with (a)ns/(b)>0%, including the high contribution species such as Abbottina rivularis (mean 5.5%) and Biwia zezera (mean 9.8%). This group (12 species) included relatively high numbers of benthic habitat use (eight species) and omnivores (nine species). The mean MDC contributions were almost zero for the group with (a)ns/(b)=0% (seven species), which included only two species of benthic habitat use and one species of omnivores. The mean MDC contributions were intermediate for the other groups with (a)negative/(b)>0% (1.30% ± 1.17%, seven species) and (a)negative/(b)=0% (0.10%, two species). The negative correlation between fish size within species and MDC contribution in groups with (a)negative/(b)>0% and (a)negative/(b)=0% indicated that ontogenetic habitat and dietary shifts induced changes in MDC transfer. Our results suggest that 21 out of 28 fish species were involved in the MDC transfer in a shallow lake, but variation in MDC transfer could be explained by fish traits (trophic guild and habitat use). Although the mean MDC contribution to all fish species was low (0.61% ± 1.97%), the roughly estimated annual consumption rate of fish on MOB corresponded to approximately 10% of the MOB production in the sediment, suggesting that fish contribute to methane dynamics from the perspective of biogeochemical cycles.