While the potential nanotoxicity of carbon nanomaterials likely renders them unsafe for environmental purification applications, it is still a daunting challenge to clarify the specific driving force for water pollutant capturing. We here employ the well-documented, mussel-inspired, environmentally safe, and biocompatible polydopamine (PDA) to modify the surface of carbon nanotubes (CNTs) which are typical carbon nanomaterials with potential toxicity. The PDA modification extents are finely tuned by adjusting the dopamine-to-CNT ratio, and the optimized modification is achieved in terms of the homogenous formation of the PDA sheath on the CNT surface (corresponding to the 0.4 PC sample). While a limited modification likely causes the surface of bare CNTs to be insufficiently covered by PDA, the excessive modification lowers the adsorption capacity per unit mass of adsorbent. The homogenous modification with PDA bearing different kinds of adsorption sites at the atomic scale makes the isothermal adsorption of Rhodamine B (RhB) suitable to be described by both the Langmuir and Freundlich models, with the maximum monolayer adsorption capacity estimated to be 266.7 mg/g. Besides, the 0.4 PC-based adsorption of RhB is dictated by chemisorption and verified to be a spontaneous, endothermic, entropy-gaining, anti-interference (against common metal cations in tap water), and repeatable process. Importantly, we disclose that hydrogen bonding is the pivotal driving force in the 0.4 PC-based adsorption process, thus enabling 0.4 PC to capture methyl orange (MO) bearing a charge state opposite to RhB, with equilibrium adsorption capacities calculated to be 135 and 159 mg/g for MO and RhB, respectively.