Attributes of 25 headwater streams and their associated wetlands were quantitatively sampled in the inner coastal plain of eastern North Carolina. Data from these sites were used to construct and test one functional assessment model (biogeochemical cycling) using the hydrogeomorphic (HGM) approach. Of the 25 sites sampled, 16 unaltered sites were used to establish standards against which field indicators could be compared (indexed). Nine altered sites were used to examine the sensitivity of the model to assess the types of alterations typically inflicted upon headwater ecosystems in eastern North Carolina: channelization, logging, construction of cross-floodplain ditches to shunt water directly from uplands to the main stream channel, and conversion of stream floodplains and buffer zones to cropland. Of 30 field indicators measured that potentially could be used to model alterations to hydrologic regime and biomass stocks, we found six were robust in assessing conditions related to biogeochemical cycling. Hydrologic indicators used in the model included: (1) presence/absence of channelization, (2) presence/absence of cross-floodplain ditches, and (3) a measure of buffer condition (using width and quality). Biomass indicators included: (4) total basal area of trees, (5) percent litter cover, and (6) volume of coarse woody debris. Our preliminary biogeochemical cycling model using these six variables was sensitive to alterations in nine altered sites and to a suite of hypothetical restorations of the most altered site. However, in order to improve accuracy of our preliminary model, it should be validated with studies designed to measure how alterations of various types and magnitudes affect biogeochemical processes.