Primary production, planktonic respiration, bacterial abundance, and chlorophyll a were measured in the epilimnion of two Canadian Shield lakes and in two large rivers to establish their metabolic balance and to contrast oligotrophic and oligo-mesotrophic systems. Pronounced diel respiration cycles were observed in all systems, with a minimum in the morning and a maximum in the evening. Respiration was positively correlated with water temperature, incident light, and chlorophyll a concentration. Diel cycles of chlorophyll a were discernible in both rivers and in the oligo-mesotrophic lake. Our results show that a single morning sampling underestimates both respiration and chlorophyll a, whereas a single sample taken at noon generally agrees better with the average of four daily measurements. In oligotrophic Lac Croche, the photosynthetic parameter αB remained constant throughout the day, whereas PBm increased by 12.5% between 0600 h and 1300 h. Ignoring the diel community respiration cycle resulted in a ~25% underestimation of daily respiration, whereas ignoring the PBm cycle induced a ~9% underestimation of the daily primary production. The net balance between production (P) and respiration (R) of the oligotrophic lake epilimnion remained positive during two summers, and the P:R ratio showed net autotrophy for all systems except for the oligotrophic river, which was slightly net heterotrophic.