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When attempting to resolve difficult issues of statutory construction involving complex statutes, courts sometimes focus on individual words and phrases without evaluating how they fit within the text and structure of the whole statute. We call this “atomization” of the statutory text. Judges have fallen into this trap in construing the Clean Water Act (CWA) and other lengthy, complex federal environmental statutes. That tendency contributes to ongoing confusion about the scope and coverage of the CWA. During the 2019-2020 Term, the U.S. Supreme Court will resolve a circuit split in the most recent line of cases exhibiting this tendency. Courts have struggled to ascertain the scope of CWA permitting jurisdiction when pollutants reach water bodies through an intermediary conduit such as groundwater. Some courts have “atomized” that analysis, leading to further analytical confusion. Evaluating this issue in light of the functions CWA permits serve in the whole statutory scheme leads to more logical results. The “conduit” cases thus serve as a good example of the perils of atomization, and how it can be avoided through a whole text analysis. That method, in turn, can allow courts to avoid altogether separate debates about the relevance of legislative history and other non-textual indicia of congressional purpose in statutory construction.