The present work aimed to study the relationship between protein carbonylation and the loss of water-holding capacity (WHC) occurring during frozen storage of porcine muscles. Pork samples corresponding to two different muscle types, glycolytic M. longissimus dorsi (LD) and oxidative M. psoas major (PM), and subjected to two different premincing, minced (MINCED) and intact pork pieces (INTACT), and packaging, vacuum packaged (VACUUM) and packed in oxygen-permeable bags (OXYGEN), procedures were frozen (-18 °C/12 weeks) and analyzed at sampling times upon thawing (weeks 1, 4, 8, and 12) for the relative amount of specific protein carbonyls, α-aminoadipic and γ-glutamic semialdehydes (AAS and GGS, respectively), and their ability to hold water using two different techniques. The formation of protein carbonyls occurred concomitantly with the loss of WHC, and both phenomena were found to be more intense in LD muscles and in MINCED and OXYGEN pork samples. The loss in WHC was from ca. 10 to 30% in 12 weeks, depending on the method of determination. Plausible mechanisms by which protein carbonylation may decrease the WHC of pork samples are thoroughly discussed in the present paper. Besides the likely impact of protein carbonylation in the water-myofibrillar protein relationships, the implication of AAS and GGS in further reactions including plausible cross-linking would explain the decrease of these semialdehydes by the end of frozen storage and would reinforce their liability in the loss of WHC of porcine muscles. The exact nature of these reactions, however, should be investigated in further studies.