During the last decade, intensive fish farming developed along the central Croatian coast, creating a need to study and evaluate its potential influence on unaffected sites. We considered phosphorus as an indicator of the influence of fish farming and investigated the distribution of phosphorus forms in sediment from several fish farms and marine areas of different trophic status in the middle Adriatic. Analyses of samples were performed with modified SEDEX techniques. Our results indicated that authigenic apatite phosphorus showed no significant differences among the investigated stations, while organic phosphorus concentrations reflected the trophic status of the station area. Below-cage sediment was characterized by enhanced fish debris phosphorus and low detrital apatite phosphorus concentrations, while sediment from an anthropogenically influenced bay showed the highest values of iron bound phosphorus species. Among the different P fractions, fish debris phosphorus proved to be the most sensitive indicator of the influence of fish farming on marine sediment.