Mechanistic understanding of the role of transparent exopolymer particles (TEP) in particular and macrogels in general on food web functioning is an overlooked aspect of ecosystem modeling. Here, I address this problem by using a 1-dimensional, vertically resolved model that integrates particle aggregation dynamics with pelagic ecosystem structure. The model first simulates the observed annual food web structure of the mesotrophic Marmara Sea ecosystem in the absence of aggregation processes. This reference structure is reduced by about 40% in the presence of aggregation webs formed by direct physical collision of detritus particles with live phytoplankton or bacterial cells. This type of aggregation model approach therefore introduces adverse effects on the overall food web structure and is more restrictive in terms of aggregate formation. The alternative aggregation web considers transforming a fraction of dissolved organic matter into particulate form by incorporating 2 TEP size classes. They coagulate with phytoplankton and bacterial cells to form live biotic aggregates (BG) and with detritus to form abiotic (AG) aggregates; additional coagulation of AG and BG particles forms macrogels. This system results in approximately 2-fold higher aggregate concentrations, which facilitates stronger particle sedimentation to the deep sea (quantified by AG concentrations) and higher food availability for macrozooplankton (quantified by BG concentrations). It also maintains the reference food web structure with only minor changes. Therefore, the present study demonstrates the feasibility of coupling food web models with a simplified TEP-based aggregation model.