This modelling study relates dimethylsulfide emission from a microbial mat to the flux of dimethylsulfoniopropionate that is exuded into the interstitial space of the mat by phototrophs. Dimethylsulfoniopropionate may be either cleaved or demethylated. Only cleavage results in the production of dimethylsulfide, which itself is further oxidized or escapes from the mat. The fate of dimethylsulfoniopropionate depends on the functional group composition of the mat, the physiological characteristics of these groups, and the eco-physiological conditions oxic/anoxic and light/dark, which both vary in a diel cycle. These three factors are accounted for in a mathematical model of a microbial mat typical of the Wadden Islands of The Netherlands and Germany. Model simulations quantify increased dimethylsulfide production under alkaline stress as well as additional dimethylsulfoniopropionate loads.