Oxidized multi-walled carbon nanotubes (oxCNTs) were functionalized by a simple non-covalent modification procedure using quaternized hyperbranched poly(ethyleneimine) derivatives (QPEIs), with various quaternization degrees. Structural characterization of these hybrids using a variety of techniques, revealed the successful and homogenous anchoring of QPEIs on the oxCNTs’ surface. Moreover, these hybrids efficiently dispersed in aqueous media, forming dispersions with excellent aqueous stability for over 12 months. Their cytotoxicity effect was investigated on two types of gram(−) bacteria, an autotrophic (cyanobacterium Synechococcus sp. PCC 7942) and a heterotrophic (bacterium Escherichia coli). An enhanced, dose-dependent antibacterial and anti-cyanobacterial activity against both tested organisms was observed, increasing with the quaternization degree. Remarkably, in the photosynthetic bacteria it was shown that the hybrid materials affect their photosynthetic apparatus by selective inhibition of the Photosystem-I electron transport activity. Cytotoxicity studies on a human prostate carcinoma DU145 cell line and 3T3 mouse fibroblasts revealed that all hybrids exhibit high cytocompatibility in the concentration range, in which they also exhibit both high antibacterial and anti-cyanobacterial activity. Thus, QPEI-functionalized oxCNTs can be very attractive candidates as antibacterial and anti-cyanobacterial agents that can be used for potential applications in the disinfection industry, as well as for the control of harmful cyanobacterial blooms.