The bioavailability of organic contaminants adsorbed to carbon nanotubes (CNTs) remains unclear, especially in complex natural freshwaters containing natural organic matter (NOM). Here, we report on the adsorption capacity (Q0) of five CNTs exhibiting different physicochemical properties, including a single-walled CNT (SWCNTs), multiwalled CNTs (MWCNT-15 and MWCNT-30), and functionalized MWCNTs (hydroxyl, −OH, and carboxyl, −COOH), for the model polycyclic aromatic hydrocarbon phenanthrene (3.1−800 μg/L). The influence of phenanthrene adsorption by the CNTs on bioavailability and toxicity was investigated using the freshwater algae Pseudokirchneriella subcapitata. CNTs were dispersed in algal growth media containing NOM (DOC, 8.77 mg/L; dispersed concentrations: 0.5, 1.3, 1.3, 3.3, and 6.1 mg/L for SWCNT, MWCNT-15, MWCNT-30, MWCNT−OH, and MWCNT−COOH, respectively). Adsorption isotherms of phenanthrene to the dispersed CNTs were fitted with the Dubinin−Ashtakhov model. Q0 differed among the CNTs, increasing with increasing surface area and decreasing with surface functionalization. SWCNT and MWCNT−COOH exhibited the highest and lowest log Q0 (8.891 and 7.636 μg/kg, respectively). The presence of SWCNTs reduced phenanthrene toxicity to algae (EC50; 528.4) compared to phenanthrene-only (EC50; 438.3), and the presence of MWCNTs had no significant effect on phenanthrene toxicity. However, phenanthrene adsorbed to NOM-dispersed CNTs proved to be bioavailable and contribute to exert toxicity to P. subcapitata.