Water quality is intricately linked to the global water crisis since the availability of safe, clean water is essential for sustaining life and ensuring the well-being of communities worldwide. Pollutants such as industrial chemicals, agricultural runoff, and untreated sewage frequently enter rivers via surface runoff or direct discharges. This study provides an overview of the key mechanisms governing contaminant transport in rivers, with special attention to storage and hyporheic processes. The storage process conceptualizes a ubiquitous reactive boundary between the main channel (mobile zone) and its surrounding slower-flow areas (immobile zone). Research from the last five decades demonstrates the crucial role of storage and hyporheic zones in influencing solute residence time, nutrient cycling, and pollutant degradation. A review of solute transport models highlights significant advancements, including models like the transient storage model (TSM) and multirate mass transport (MRMT) model, which effectively capture complex storage zone dynamics and residence time distributions. However, more widely used models like the classical advection–dispersion equation (ADE) cannot hyporheic exchange, limiting their application in environments with significant storage contributions. Despite these advancements, challenges remain in accurately quantifying the relative contributions of storage zones to solute transport and degradation, especially in smaller streams dominated by hyporheic exchange. Future research should integrate detailed field observations with advanced numerical models to address these gaps and improve water quality predictions across diverse river systems.