The development of polymeric carriers based on partially deacetylated chitin nanowhiskers (CNWs) and anionic sulfated polysaccharides is an attractive strategy for improved vaginal delivery with modified drug release profiles. This study focuses on the development of metronidazole (MET)-containing cryogels based on carrageenan (CRG) and CNWs. The desired cryogels were obtained by electrostatic interactions between the amino groups of CNWs and the sulfate groups of CRG and by the formation of additional hydrogen bonds, as well as by entanglement of carrageenan macrochains. It was shown that the introduction of 5% CNWs significantly increased the strength of the initial hydrogel and ensured the formation of a homogeneous cryogel structure, resulting in sustained MET release within 24 h. At the same time, when the CNW content was increased to 10%, the system collapsed with the formation of discrete cryogels, demonstrating MET release within 12 h. The mechanism of prolonged drug release was mediated by polymer swelling and chain relaxation in the polymer matrix and correlated well with the Korsmeyer–Peppas and Peppas–Sahlin models. In vitro tests showed that the developed cryogels had a prolonged (24 h) antiprotozoal effect againstTrichomonas, including MET-resistant strains. Thus, the new cryogels with MET may be promising dosage forms for the treatment of vaginal infections.