An existing whole-system model based on changes in dissolved N₂ concentration was modified for lentic systems. Field validations carried out at Christie Lake in Dundas, ON and Turtle Pond in Stoney Creek, ON (Canada). New model inputs included air temperature, atmospheric pressure, relative humidity, wind velocity, and Schmidt number. Mont Carlo analysis was integrated into the model to better constrain error in model estimates of denitrification, whole-system metabolism, and greenhouse gas production. Denitrification rates ranged from -419-4415 µmol N.m-².h-¹ in Christie Lake and from 10-74 µmol N.m-².h-¹ in Turtle Pond. N₂O production ranged from 915-10,635 nmol N.m-².h-¹ in Christie Lake and from -344-131 nmol N.m-².h-¹ in Turtle Pond. The whole-system model allows for the examination of biogeochemical processes at ecologically significant temporal and spatial scales.