The preparation of carbonaceous sorbents can combine the use of waste material and the improvement of water quality. Six activated carbons prepared from different agricultural waste biomasses were tested for adsorption of norfloxacin and ofloxacin fluoroquinolone antibiotics from water. Activated carbons were prepared by conventional pyrolysis at 600 °C in a nitrogen atmosphere of ZnCl2-activated red mombin seeds (RMS), corn cob (CC), coffee husk (CH), internal and external parts of mango seeds (MSEP, MSIP), and ice cream beans (GS), which are widely available as agro-industrial biomass wastes in Latin America. The textural and surface properties of prepared activated carbons were thoroughly investigated, and the sorption mechanism was described through proper kinetic and adsorption isotherm models. Moreover, the molecular dimensions of norfloxacin and ofloxacin were estimated to consider the possible sterical shielding of micropores of the investigated activated carbons. Norfloxacin and ofloxacin were strongly adsorbed onto all investigated activated carbons. Adsorption kinetics fitted best to Elovich model, adsorption isotherms correlated best with Redlich–Peterson model. Maximum adsorption capacities, obtained from Langmuir model, were 404 mg·g−1 for norfloxacin and 380 mg·g−1 for ofloxacin. The best adsorption performance was observed for RMS-based activated carbon. A comparison of prepared materials led to the conclusion that high micropore volume and net pore volume are the determining properties of good adsorption performance in the case of removal of fluoroquinolone antibiotics from water.