The rennet coagulation of milk has been extensively studied. Mathematical modeling of the gelation process has been performed, mainly for the purpose of predicting the gel point. Rheological profiles of rennet gels during aging (long reaction times) have indicated that the gel stiffness (modulus) attains a maximum and thereafter decreases. We wanted to model this type of behavior and used the Carlson model, which includes terms for the proteolysis of κ-casein hairs (creating active sites) and the crosslinking of these activated sites. To account for the observed decrease in the gel modulus with time, we modified the Carlson model by adding an exponential decay term, which we ascribe to endogenous syneresis. We believe that this decay (i.e., syneresis rate) would likely be influenced by the mobility of bonds within casein micelles (in gels as indicated by the rheological loss tangent parameter). To modify the internal structural bonding of casein micelles, reconstituted skim milk was acidified to pH values 6.4, 6.0, 5.8, 5.6, and 5.4, or EDTA was added to milk at concentrations of 0, 2, 4, and 6mM, and the final pH values of EDTA-treated samples were subsequently adjusted to pH 6.0. These treatments were then used to prepare rennet gel samples that were monitored by dynamic low amplitude oscillatory rheometry. When the modified Carlson model was fitted to the actual experimental storage modulus values of each sample, it fitted the data reasonably well (especially the pH trial data). As the pH values of milk decreased, the modulus values at infinite reaction time (G′∞) increased; however, G′∞ decreased with an increase in the EDTA concentration. In the pH trial, the rate constants for the proteolysis of κ-casein hairs and the crosslinking of these activated sites exhibited a maximum at pH 5.6 and 6.0, respectively. The rate constant for endogenous syneresis increased at pH values <6.0. The rate constant for endogenous syneresis was significantly positively correlated (r≥0.96) with the loss tangent values of gels (indicating greater mobility), probably due to the loss of insoluble calcium phosphate crosslinking within micelles, which was significantly negatively correlated (r≥0.81) with the rate constant for endogenous syneresis. In the EDTA trial, with an increase in the EDTA concentration no maximum was observed in the rate constants related to proteolysis of κ-casein hairs or crosslinking of these activated sites. The rate constant for endogenous syneresis decreased at higher EDTA levels. The different rheological/modeling behavior in the EDTA trials was likely due to the very significant inhibition of rennet gelation induced by the use of EDTA, which also resulted in extremely long reaction times. Our modified Carlson model fit our experimental pH trial data very well, which indicates that the rennet gel system has the potential to synerese from the start; indeed this ability is an innate property of the casein micelle. Endogenous syneresis was enhanced by the loss of insoluble calcium phosphate crosslinking within casein micelles as this increased bond mobility within rennet gels.