Mesoporous Silica Nanoparticles (MSNs) have been increasingly investigated as versatile drug delivery carriers. A particular challenge for the systemic use of MSNs lies in the control of their degradation, which has not been fully understood until now. We implemented standard dynamic light scattering (DLS) experiments and introduced a novel DLS technique in a confocal volume to track the dynamics of large-pore MSN degradation in situ. This unique DLS technique, which involves a small observation volume, was chosen for its ability to count particle by particle during the degradation process, a method that has not been commonly used in nanoparticle research. The experiments were performed in different media compositions at low particle concentrations, below the silica solubility limit. MSNs with large conical pores were prepared and studied as they offer the possibility to incorporate and release large-sized biomolecules. Large-pore MSNs followed a singular degradation mechanism following a stochastic-like behavior, a finding that challenges the common idea that all nanoparticles (NPs) degrade similarly and homogeneously over time. We showed that some NPs are observed intact over a prolonged period while most other NPs have already vanished or been transformed into swollen NPs. Thus, a heterogeneous degradation process occurs, while the total concentration of NPs undergoes an exponential decay. These large conical pores MSNs will be utilized as reliable biomolecule nanocarriers by predicting the factors underlying the NP hydrolytic stability.