While research has extensively investigated the dynamics of CO2 water partial pressure (pCO2) and planktonic food webs (PFWs) separately, there has been limited exploration of their potential interconnections, especially in marsh typologies. This study’s objectives were to (1) investigated if pCO2 and atmospheric CO2 flux can be elucidated by PFW topologies, and (2) ascertain if these potential relationships are consistent across two distinct “Blue Carbon” ecosystems. Abiotic and biotic variables were measured in two contrasting wetlands at the Atlantic French coast: a saltwater (SM, L’Houmeau) and a freshwater marsh (FM, Tasdon). SM acted as a weak carbon source, with pCO2 between 542 and 842 ppmv. Conversely, FM exhibited strong atmospheric CO2 source or sink characteristics, varying with seasons and stations, with pCO2 between 3201 and 114 ppmv. Five PFW topologies were linked to varying pCO2 across the two ecosystems: three stable topologies ('biological winter', 'microbial', 'multivorous' PFW) exhibited consistently high pCO2 values (FM: 971, 1136, 3020 ppmv; SM: 'biological winter' not observed, 842, 832 ppmv), while two transient topologies ('weak multivorous' and 'weak herbivorous') displayed lower and more variable pCO2 values (FM: from 127 to 1402 ppmv; SM: from 638 to 749 ppmv). Seasonality emerged as an influencing factor for both pCO2 dynamics and PFW. However, PFW in FM did not demonstrate a seasonal equilibrium state, potentially hindering a clearer understanding of the relationship between pCO2 and PFW. This is the first documented association between PFW topologies and pCO2 dynamics in “Blue Carbon” marsh environments.