Phosphorus (P) is a vital nutrient for sustaining natural water productivity. Both particulate and dissolved forms of organic and inorganic P are potentially important sources of bioavailable P for primary and secondary producers. A microcosm system to imitate the bacterial community in Plym river sediment and pore water is described and bacterial uptake rates for inorganic and organic phosphorus are presented in this paper. The aim of this study was to investigate the uptake of two organic phosphorus compounds (phytic acid and D-glucose-6-phosphate) by freshwater bacteria. The bioreactors comprise glass columns packed with two types of small glass beads on which bacterial biofilm can develop. The glass beads with different porosity were introduced to simulate River SPM. The selected P compounds spiked into the inflow of the microcosm, and measured the step change of P concentration in the outflow to investigate the behavior of bacterial uptake of nutrients. The results showed that organic phosphorus was converted into inorganic phosphorus but the conversion rate depended on the type of phosphorus species. One experiment suggested that phytic acid (refractory) could displace phosphate from the biofilm surface; the other experiment showed that D-glucose-6-phosphate (labile) could be hydrolysed and utilized easily by the bacteria. The results also suggested that bacteria might break down the C-P bonds to utilize the carbon. Further experiments should investigate the effect of varying the C:N:P ratio in the microcosm system to determine which nutrient limits bacteria uptake.