Lakes process terrigenous carbon. The carbon load processed by lakes may partially offset estimates made for terrestrial net ecosystem exchange (NEE). The balance within the lake between sedimentation and flux to the atmosphere determines whether lakes are net sinks or net sources of atmospheric carbon. Here we develop a model to study carbon processing by lakes, and calibrate the model to a range of lake conditions found in northern Wisconsin. Our model indicated that lakes processed from 3-14% of terrestrial NEE, venting most of that carbon to the atmosphere. Most lakes were net heterotrophic and net sources of carbon to the atmosphere. When considering lakes over gradients of TP and DOC, only those lakes low in DOC and moderate to high in TP were net autotrophic and net sinks of carbon from the atmosphere. The model was especially sensitive to two parameters that may respond to drivers not included in the model: planktivory effects on algal biomass and pH changes due to acid deposition reductions.