Pharmaceuticals including antibiotics are among the hazardous micropollutants (HMP) of the environment. Incomplete degradation of the HMP leads to their persistence in water bodies causing a plethora of deleterious effects. Conventional wastewater treatment cannot remove HMP completely and a promising alternative comprises biotechnologies based on microalgae. The use of immobilized microalgae in environmental biotechnology is advantageous since immobilized cultures allow the recycling of the microalgal cells, support higher cell densities, and boost tolerance of microalgae to stresses including HMP. Here, we report on a comparative study of HMP (exemplified by the antibiotic ceftriaxone, CTA) removal by suspended and chitosan-immobilized cells ofLobosphaerasp. IPPAS C-2047 in flasks and in a column bioreactor. The removal of CTA added in the concentration of 20 mg/L was as high as 65% (in the flasks) or 85% (in the bioreactor). The adsorption on the carrier and abiotic oxidation were the main processes contributing 65–70% to the total CTA removal, while both suspended and immobilized cells took up 25–30% of CTA. Neither the immobilization nor CTA affected the accumulation of arachidonic acid (ARA) byLobosphaerasp. during bioreactor tests but the subsequent nitrogen deprivation increased ARA accumulation 2.5 and 1.7 times in the suspended and chitosan-immobilized microalgae, respectively. The study of theLobosphaerasp. microbiome revealed that the immobilization of chitosan rather than the CTA exposure was the main factor displacing the taxonomic composition of the microbiome. The possibility and limitations of the use of chitosan-immobilizedLobosphaerasp. IPPAS C-2047 for HMP removal coupled with the production of valuable long-chain polyunsaturated fatty acids is discussed.