Understanding the behavior of secondary minerals under alkaline conditions is important for predicting the potential alteration of the constituent minerals in radioactive-waste disposal facilities. A previous study reported the formation of uncommon Fe- and Mg-bearing clays under natural alkaline conditions in the Philippines; these were referred to as iron-magnesium-silicate-hydrates (F-M-S-H) and nontronite-like minerals. The current study aimed to investigate the structural and chemical characteristics and to understand the formation pathways of these clays by performing a detailed characterization. F-M-S-H comprised tetrahedral–octahedral–tetrahedral (TOT) layers, imperfect interlayer hydroxide sheets, and interlayer Ca ions. The systematic changes in the characteristics of F-M-S-H at different sampling depths, such as the gradual decrease of the interlayer hydroxide sheets to form smectitic domains, were caused by the differing interaction periods between each sediment at different sampling depths and alkaline seepage. Furthermore, F-M-S-H was ferrous in form prior to oxidation. In contrast, a nontronite-like mineral comprised nontronite and part of an interlayer hydroxide sheet. This mineral was inferred to be formed under chemically different conditions from F-M-S-H, and probably formed in the presence of aqueous Fe3+ and Mg ions.