This study investigated the growth rate of chitosan-immobilized cells of the marine cyanobacterium Synechococcus elongatus and its potential application in the removal of nitrogen and phosphorus for wastewater treatment. Immobilized cell cultures had a lag phase of growth due to the immobilization method, and their growth rate was similar to that of free-living cell cultures. Ammonia removal was higher in free cells (54%) than in immobilized cells (29%), but nitrate removal was similar in immobilized (38%) and free cells (44%); phosphorus removal was more efficient in free cells (88%) than in immobilized cells (77%). Chlorophyll a and protein content were higher in immobilized cells. Our study demonstrates that S. elongatus immobilized into chitosan capsules can remove nutrients and is able to maintain a growth rate comparable to that of free cells in culture.