Stream assessment tools and models are essential to inform regulatory decisions, mitigation and restoration design, status and trend analyses, and other management practices. Diverse stream assessment tools, models, and methods have been created to address specific management contexts and regional needs. However, the vast number of methods available, the difficulty in comparing results across different approaches, and the need to balance effort with available resources has led to challenges in assessing stream ecosystem conditions. We introduce a model for stream assessment to address these key challenges by standardizing assessment across different tiers and methodologies. The model integrates functions-based and physical habitat-based models, capturing the full spectrum of stream functions and processes and reflecting the interconnectedness of stream functions and processes. This model is designed to be comprehensive and standardized to help improve consistency and comparability of assessments, enhance understanding of stream conditions, and inform interventions that promote the health and sustainability of water resources. The model consists of three layers: a variables layer containing stream functions, an organizational layer that acts as an organization and communication tool, and an analytical layer for ecological indices for reporting and decision-making. The analytical layer of the model is aligned with the goals of the Clean Water Act to increase the model’s utility and regulatory relevance. The model’s scoring system and aggregation methods facilitate clear communication of results, aiding decision-making and policy development. Continuous collaboration with the scientific community and practitioners will be needed to refine the list of functional variables, validate and improve model performance, and test and refine the model, as well as exploring the incorporation of emerging issues such as the effects of climate change on stream functions.