The present dataset relates to an experiment studying the impacts of particles on chromophoric dissolved organic matter (CDOM) dynamics by comparing three scenarios: a particle-free environment, a particle-enriched system with polystyrene microplastics, and a particle-enriched system with inorganic particles (water insoluble SiO₂). In experimental part 1 of the experiment, natural marine organic matter was obtained by culturing a non-axenic strain of Chaetoceros socialis in 2 L flasks under each of three scenarios (1C = control, 2PS = polystyrene, 3S = silica). The first dataset reports cell numbers per each 2 L flask for experimental part 1.Subsequently, in experimental part 2, filtered samples from the three flasks containing dissolved organic matter and bacteria were incubated separately in the dark in separate cuvettes (4 replicates per each scenario) for 5 days to monitor changes in dissolved organic matter. In this phase, Chromophoric dissolved organic matter (CDOM), a bulk optical property, was monitored daily to examine changes in its quality and quantity and to compare degradation dynamics in the three systems (1C, 2PS and 3S). The dataset for part 2 reports CDOM absorption coefficient at 355 nm (a355, m^-1^), estimated Dissolved Organic Carbon (DOC, µM), as well as spectral slope parameters in different wavelengths as indicators of CDOM degradation processes and microbial activity: spectral slope Sbetween 302 and 322 nm (S302-322, nm^-1^), between 275 and 295 nm (S275-295, nm^-1^), and between 350 and 400 nm (S350-400, nm^-1^), as well as slope ratio SR, as SR = S275-295:S350-400.At the beginning of experimental part 2 (on day t7), oxygen concentrations were also measured in each cuvette of all of the three scenarios 1C, 2PS and 3S.