Lake respiration is supported by a mixture of autochthonous and allochthonous resources, but the relative significance and interaction of these sources are uncertain across gradients of primary production and organic matter inputs. We manipulated autochthonous resources by adding inorganic nitrogen and phosphorus to two lakes during three summers and monitored a third reference lake. Allochthonous resources were measured as fluorescent dissolved organic matter (FDOM). In the reference and two experimental lakes, daily estimates of respiration were made from continuously deployed oxygen sensors. Daily mean values of temperature and FDOM were determined from high‐frequency measurements along with daily measures of chlorophyll a, an index of phytoplankton biomass. We analyzed time series of respiration and tested models that used combinations of the independent variables chlorophyll, FDOM, and temperature. The best models included all three of the independent variables. Respiration increased twofold over the temperature range of 14.5–28.6°C. Respiration increased in association with phytoplankton blooms caused by the nutrient additions, but did not track blooms closely, because of large day‐to‐day variability. Respiration varied positively with FDOM that was primarily allochthonous and differed among lakes and years. We did not detect an interaction between chlorophyll and FDOM despite the large number of observations and range of chlorophyll and FDOM. Hydrologic, climatic, and land use changes are altering temperature and inputs of nutrients and organic matter to lakes. Our results indicate that these changes may lead to linear responses in ecosystem processes like respiration for the wide range of inputs represented in this study.