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Abstract It is critical to understand how human modifications of Earth’s ecosystems are influencing ecosystem functioning, including net and gross community production ( NCP and GCP , respectively) and community respiration ( CR ). These responses are often estimated by measuring oxygen production in the light ( NCP ) and consumption in the dark ( CR ), which can then be combined to estimate GCP . However, the method used to create “dark” conditions—either experimental darkening during the day or taking measurements at night—could result in different estimates of respiration and production, potentially affecting our ability to make integrative predictions. We tested this possibility by measuring oxygen concentrations under daytime ambient light conditions, in darkened tide pools during the day, and during nighttime low tides. We made measurements every 1–3 months over one year in southeastern Alaska. Daytime respiration rates were substantially higher than those measured at night, associated with higher temperature and oxygen levels during the day and leading to major differences in estimates of GCP calculated using daytime versus nighttime measurements. Our results highlight the potential importance of measuring respiration rates during both day and night to account for effects of temperature and oxygen—especially in shallow-water, constrained systems—with implications for understanding the impacts of global change on ecosystem metabolism.