Coastal terrestrial–aquatic interfaces (TAIs) are dynamic zones of biogeochemical cycling influenced by salinity gradients. However, there is significant heterogeneity in salinity influences on TAI soil biogeochemical function. This heterogeneity is perhaps related to unrecognized mech- anisms associated with carbon (C) chemistry and micro- bial communities. To investigate this potential, we evaluated hypotheses associated with salinity-associated shifts in or- ganic C thermodynamics; biochemical transformations; and nitrogen-, phosphorus-, and sulfur-containing heteroatom or- ganic compounds in a first-order coastal watershed on the Olympic Peninsula of Washington, USA. In contrast to our hypotheses, thermodynamic favorability of water-soluble or- ganic compounds in shallow soils decreased with increas- ing salinity (43–867 μS cm−1 ), as did the number of in- ferred biochemical transformations and total heteroatom content. These patterns indicate lower microbial activity at higher salinity that is potentially constrained by accumula- tion of less-favorable organic C. Furthermore, organic com- pounds appeared to be primarily marine- or algae-derived in forested floodplain soils with more lipid-like and protein-like compounds, relative to upland soils that had more lignin-, tannin-, and carbohydrate-like compounds. Based on a re- cent simulation-based study, we further hypothesized a re- lationship between C chemistry and the ecological assembly processes governing microbial community composition. Null modeling revealed that differences in microbial community composition – assayed using 16S rRNA gene sequencing – were primarily the result of limited exchange of organisms among communities (i.e., dispersal limitation). This results in unstructured demographic events that cause community composition to diverge stochastically, as opposed to diver- gence in community composition being due to determinis- tic selection-based processes associated with differences in environmental conditions. The strong influence of stochastic processes was further reflected in there being no statistical re- lationship between community assembly processes (e.g., the relative influence of stochastic assembly processes) and C chemistry (e.g., heteroatom content). This suggests that mi- crobial community composition does not have a mechanis- tic or causal linkage to C chemistry. The salinity-associated gradient in C chemistry was, therefore, likely influenced by a combination of spatially structured inputs and salinity- associated metabolic responses of microbial communities that were independent of community composition. We pro- pose that impacts of salinity on coastal soil biogeochemistry need to be understood in the context of C chemistry, hydro- logic or depositional dynamics, and microbial physiology, while microbial composition may have less influence.