Nanoporous anodic titanium dioxide (ATO) layers on Ti foil were prepared via a three step anodization process in an electrolyte based on an ethylene glycol solution with fluoride ions. Some of the ATO samples were heat-treated in order to achieve two different crystallographic structures – anatase (400 °C) and a mixture of anatase and rutile (600 °C). The structural and morphological characterizations of ATO layers were performed using a field emission scanning electron microscope (SEM). The hydrophilicity of ATO layers was determined with contact angle measurements using distilled water. Ibuprofen and gentamicin were loaded effectively inside the ATO nanopores. Afterwards, an in vitro drug release was conducted for 24 h under a static and dynamic flow conditions in a phosphate buffer solution at 37 °C. The drug concentrations were determined using UV–Vis spectrophotometry. The absorbance of ibuprofen was measured directly at 222 nm, whether gentamicin was determined as a complex with silver nanoparticles (Ag NPs) at 394 nm. Both compounds exhibited long term release profiles, despite the ATO structure. A new release model, based on the desorption of the drug from the ATO top surface followed by the desorption and diffusion of the drug from the nanopores, was derived. The proposed release model was fitted to the experimental drug release profiles, and kinetic parameters were calculated.