This paper deals with a comparative study on the interpolymeric complexes of alginate poly(N-isopropyl acryl amide (PNIPAAm) and corresponding graft copolymers with various compositions in respect to their toxicity, biocompatibility and in vitro and in vivo release of theophylline (THP). Loading of the various matrices with theophylline and characterization of loaded matrices was studied by near infrared spectroscopy–chemical imaging (NIR–CI) analysis, scanning electron microscopy (SEM) and thermogravimetric analysis (TGA). It was appreciated that THP loading is higher than 40% and the drug is relatively homogeneous distributed within all matrices because of some specific interactions between components of the system. All samples have been found to be non-toxic and biocompatible. It was established that graft copolymers having a good stability show a better drug carrier ability, a higher THP loading, a prolonged release (longer release duration for graft copolymers of 235.4–302.3 min than that for IPC 72/28 of 77.6 min, which means approximately four times slower release from the graft copolymer-based matrices than from the interpolymeric complex) and a good bioavailability. The highest values for THP loading (45%), prolonged release (302.3 min) and bioavailability (175%) were obtained for graft copolymer AgA-g-PNIPAAm 68. The drug release mechanism varies with composition and architecture of the matrix.