The data were collected from an experiment using phytoplankton cultures (Apocalathium malmogiense and Rhodomonas marina). The aim of the experiment was to study carbon cycling among phytoplankton and bacteria, and the effects on the dissolved organic matter (DOM) pool. Measured variables include phytoplankton and bacterial abundance, primary production, bacterial production and respiration, 14C-transfer from phytoplankton to DOM and bacteria, concentrations of particulate and dissolved organic carbon, nitrate, phosphate and chlorophyll a, and optical characteristics of dissolved organic matter. The experiment was conducted at Tvärminne Zoological Station, Hanko, Finland with non-axenic unialgal phytoplankton cultures and bacteria originating from the Baltic Sea. The experiment was conducted between Dec. 2017 and Apr. 2018. The experiment consisted of two parts, the DOM release experiment (part 1) and the DOM consumption experiment (part 2). Separate triplicate batch cultures of both phytoplankton species were grown for each experiment. In the DOM release experiment the cultures were grown for over 4 months and three day-long incubations (key point incubations, KPI's) were initiated on three occasions; the first KPI at early exponential growth phase and the second and third KPI's when the phytoplankton had grown more abundant. During each KPI and aliquot of the culture was inoculated with freshly collected sea water bacteria, and bacterial community composition was measured. This aliquot was then divided into two further aliquots; one was incubated with radioisotopes for productivity (primary and bacterial production) and 14C-flow analyses (production line) and one filtered through 0.8 µm for analysis of DOM optical properties. During the KPI's measurements were taken at 0, 4, 8 and 12 h. Nutrient concentrations (measured from non-filtered and 0.8 µm filtered samples) and concentration of dissolved organic carbon were measured only at 0 and 12 h. Concentrations of particulate organic carbon and nitrogen and chlorophyll a were measured only once for each KPI at the beginning of the incubation. In the DOM consumption experiments the cultures were grown to high abundance, after which the phytoplankton and most of the bacteria were filtered out. The filtrate was then inoculated with freshly collected sea water bacteria, after which it was incubated for 7 days. Bacterial abundance, production, respiration, and community composition, and concentration and optical properties of DOM were measured daily. The experimental design is explained in figure 1 of the associated publication.This data table contains the measurements taken during the KPIs of part 1 (DOM release experiment). Measurements are shown for all replicates (Replicate) of both phytoplankton treatments (Species) at each KPI (Exp run) at each measurement time point of the incubation (Inc dur). The measured variables include concentrations of nitrate, phosphate, chlorophyll a, particulate organic carbon and nitrogen, dissolved organic carbon, and total inorganic carbon, primary production, incorporation rates of 3H-thymidine and 14C-leucine and bacterial production calculated based on these, abundance of high and low nucleic acid and total bacteria, flow cytometric side scatter of high and low nucleic acid bacteria, optical properties of DOM, phytoplankton abundance, abundance of A. malmogiense cells with lower chlorophyll a fluorescence, and percentage of phytoplankton cells with intact membranes. Primary production is calculated using two subsamples incubated in light, and one subsample incubated in dark, and the dark measurement was subtracted from the mean of the light measurements. These light and dark samples were also used for calculating bacterial production and the 14C-flow (table 2 of the associated publication). For measurements taken in these light and dark samples (i.e. production line) see https://doi.pangaea.de/10.1594/PANGAEA.937723.