Data sets are outputs of two experiments (each experiment includes two or more temporally replicated trials - named by date) that were conducted using a newly developed Fluorometer and Oximeter equipped Flow-through Setup (FOFS).The corresponding method paper is titled 'Simultaneous recording of filtration and respiration in marine organisms in response to short-term environmental variability'. The paper is under review by Limnology and Oceanography: Methods.The main directory of experimental data (e.g., FOFS_test/blank_trials) contain subdirectories termed raw_data_temperature (including °C-temperature .xlsx files), raw_data_Chl, and raw_data_Oxygen, the two latter contains folders named after the starting dates of the trials (e.g., 04_nov).Each of these folders has three subfolders named after the three stages of the trial (i.e., pre, main, and post). Each subfolder includes data sheets of mV-Chl (.CSV) or %air-saturation (.xlxs, which are outputs of the DO calulator.py) that were collected in the corresponding stage and trial.The data can be processed through the Python scripts accompanying the method paper, providing time-series of filtration, respiration, and scope for growth along daily thermal cycles for the studied blue mussel Mytilus spp. specimens (see the paper for details).