To study the structure and function of soil organic matter, soil scientists have performed alkali extractions for soil humic acid (HA) and fulvic acid (FA) fractions for more than 200 years. Over the last few decades aquatic scientists have used similar fractions of dissolved organic matter, extracted by resin adsorption followed by alkali desorption. Critics have claimed that alkali-extractable fractions are laboratory artifacts, hence unsuitable for studying natural organic matter structure and function in field conditions. In response, this review first addresses specific conceptual concerns about humic fractions. Then we discuss several case studies in which HA and FA were extracted from soils, waters, and organic materials to address meaningful problems across diverse research settings. Specifically, one case study demonstrated the importance of humic substances for understanding transport and bioavailability of persistent organic pollutants. An understanding of metal binding sites in FA and HA proved essential to accurately model metal ion behavior in soil and water. In landscape-based studies, pesticides were preferentially bound to HA, reducing their mobility. Compost maturity and acceptability of other organic waste for land application were well evaluated by properties of HA extracted from these materials. A young humic fraction helped understand N cycling in paddy rice (Oryza sativa L.) soils, leading to improved rice management. The HA and FA fractions accurately represent natural organic matter across multiple environments, source materials, and research objectives. Studying them can help resolve important scientific and practical issues.