To determine the effects of intensive cropping of tropical lowland rice (Oryza sativa L.) and the associated long-term soil submergence on chemical properties of soil organic matter, we used solid-state 13C and 15N and solution 31P nuclear magnetic resonance (NMR) spectroscopy to analyze the labile mobile humic acid (MHA) and the more recalcitrant calcium humate (CaHA) fractions extracted from a series of soils supporting several long-term field experiments in the Philippines. The soils varied mainly in degree of submergence and cropping intensity, ranging from a rainfed rice field without soil submergence to irrigated double- and triple-cropped fields in which soil remains submerged almost all year long. As reported previously, all analyses associated increasing intensity of rice cropping with larger proportions of less humified material in the MHA and CaHA, such as diester phosphorus (P), amide nitrogen (N), and phenolic carbon (C). We established significant correlations between proportions of various spectral areas as well as between some spectral areas and other humic acid (HA) properties such as visible light absorption and free radical concentration (positive indices of humification) and hydrogen (H) concentration (negative index of humification). For example, spectral proportions of heterocyclic N were positively, and proportions of amide N and phenolic C negatively, correlated with visible light absorption and free radical concentration, and each of these spectral proportions had an opposite sign when correlated with H concentration. The correlations of N-alkyl C proportions were the strongest with these properties and with other functional group proportions.