Scientific concepts and measurements that relate soil and water resources are lacking in several areas, limiting our development of a framework or nexus to assess soil–watershed health. Current research designs rely on land management practices as a proxy for soil condition. Yet, conservation practices are often studied in isolation of each other, and adoption may be driven by state and federal farm programs that can incentivize a given management practice without accounting for current, novel farmer‐driven adoption of conservation systems. Despite the value of conservation management, its ability to predict soil health is often limited if based solely on land management because chemical, physical, and biological processes vary across time, discipline, and terrain. Similarly, connections between soil health and water quality are constrained due to several “grand challenges” that include dissimilar scales and the number of metrics required to correlate soil and water systems. Equally important is soil sampling within the critical flow path(s) that determines sediment/contaminant loading. In some instances, most of the sediment/contaminant loading during a portion or entire year results from channel and bank erosion and not overland flow that may not be within conservation management hectares. Additional challenges include legacy effects of prior land management, climate variability, and varying turnover rates of soil and water systems. This special section aims to frame research issues that inspire new approaches and collaborations for tackling the challenge of leveraging soil health to strengthen water management across plot, field, and watershed scales, using models, statistics, and other novel methodologies.