Summary1. Despite the recognition of its importance, benthic primary production is seldom reported, especially for large lakes. We measuredin situbenthic net primary production by monitoring flux in dissolved inorganic carbon (DIC) concentration in benthic incubation chambers, based on continuous measurements of CO2(aq)flux, alkalinity, and the temperature‐dependent dissociation constants of carbonic acid (K1andK2). This methodology has the advantages of monitoring net primary production directly as change in carbon, maintaining continuous water recirculation, and having sufficient precision to detect change in DIC over short (i.e. 15 min) incubations, even in alkaline waters.2. Benthic primary production onCladophora‐dominated rocky substrata in western Lake Ontario was measured biweekly. Maximum biomass‐specific net photosynthetic rates were highest in the spring (2.39 mgC g Dry Mass−1 h−1), decreased to negative rates by early summer (−0.76 mgC g DM−1 h−1), and exhibited a regrowth in late summer (1.98 mgC g DM−1 h−1).3. ACladophoragrowth model (CGM), previously validated to predictCladophorabiomass accrual in Lake Ontario, successfully simulated the seasonality and magnitude of biomass‐specific primary production during the first cohort ofCladophoragrowth. Averaged over this growing season (May–Aug), mean areal net benthic production at the estimated depth of peak biomass (2 m) was 405 mg C m−2 d−1.4. We measured planktonic primary production in proximity to the benthic study and constructed a depth‐resolved model of planktonic production. Using the CGM, benthic primary production was compared with planktonic primary production for the period May–Aug. Net benthic production from the shoreline to the 12 m contour (1–2 km offshore) equalled planktonic production. Closer to shore, benthic primary production exceeded planktonic primary production. Failure to account for benthic primary production, at least during abundantCladophoragrowth, will lead to large underestimates in carbon and nutrient flows in the nearshore zone of this Great Lake.