The absorption of organic dyes from aqueous medium by vertically aligned carbon nanotubes (VA-CNTs) is an ongoing research topic, as these nanostructures present outstanding physical and chemical properties that may favor their interaction with organic pollutants. The growth temperature variation yields different VA-CNT surface morphologies ranging from wave-like patterns to patternless or planar patterns. Here, we demonstrate the effect of the interaction between the intrinsic oxygen concentration of the VA-CNTs grown at different temperatures (650 °C and 700 °C) on the adsorption of cationic (Rhodamine B - RhB) and anionic (Methyl Orange - MO) dyes from aqueous media through UV-vis spectrophotometry studies. The XPS technique was applied to estimate the oxygen percentage (O at%) present on the nanotubes as follows: 0.62% on the wavy patterned VA-CNTs and 2.32% on VA-CNTs without a pattern. The highest adsorption performance was accomplished by VA-CNTs without a pattern for RhB dye, attributed to electrostatic interactions, where the positively charged RhB is attracted to the negatively charged nanotube surface. In this way, VA-CNTs have shown adsorption characteristics crucial for wastewater decontamination.