A benthic chamber system was developed to measure all major nitrogen cycling processes in lakes. The system coupled advantages of flow-through systems common in core incubations with those of in situ benthic chambers. The system also coupled advantages of N2:Ar and isotope pairing techniques for explicit measurement of gross and net denitrification, allowing determination of N2 fixation. Use of 15N tracer (15N2, 15NO3-, or 15NH4+), in these chambers also allowed explicit and simultaneous in situ measurements of other major nitrogen cycling processes including ammonium and nitrate uptake, DNRA, and ammonification.Nutrient loading ratios (Si:N and P:N) and community composition of herbivores (Daphnia and mussels) were studied to determine effects on nitrogen cycling using mesocosms simulating thermally stratified, shallow lakes. Increased Si:N enhanced organic matter remineralization in bottom water, enhancing nitrogen loss by denitrification. Herbivore type had no apparent effect on where N was recycled or on N-loss through denitrification.