The persistence of potential tracers of dissolved organic matter (DOM) generated from farm waste-amended soil was investigated by fluorescence spectroscopy coupled with classification and regression tree (CART) and principal component analysis (PCA) during a short-term (8 days) to midterm (60 days) biodegradation study. Pig manure (PM), cow manure (CM), wheat straw (WS), and soil alone (SA) treatment inputs were used. Waste amendments were potential sources of higher DOM concentrations. PCA revealed the DOM quality differences between farm wastes and soil alone as well as a significant shift observed from the biochemical to the geochemical fluorescent fraction in SA and PM treatments. The tryptophan:Humic-Like ratio and tryptophan zone were the potential discriminators of recent and midterm pollution by farm wastes. Integral intensities of the Fulvic-Like zone and region III discriminated the PM from CM and WS during the 60 days. CART analysis showed 90 and 100% potential for farm wastes discrimination from soil during P1 and P2, respectively. The prediction successes were 72 and 57% for PM from other wastes and 60 and 100% for WS during both periods. Fluorescence spectroscopy in combination with CART analysis can be a nondestructive innovative method for monitoring susceptible farm waste contamination.