Wastewater-based epidemiology (WBE) has become crucial for early microbial outbreak detection and public health surveillance globally, underscored by the COVID-19 pandemic. However, despite advancements in sampling and analyses, interpreting results and estimating infection rates pose challenges. Enhancements in sewer system engineering, understanding the wastewater environment, and addressing the impact of the environment on the accuracy of results are needed. Objective: This scoping review aims to identify engineering knowledge gaps in WBE to guide future study designs. Design: Research on “wastewater-based epidemiology” involving “engineering”, published between 2015 and 2023, was extracted from the Scopus database. Results: This scoping review examines elements influencing WBE’s precision and reliability, especially in identifying and measuring SARS-CoV-2 RNA. It identifies significant effects of engineering, analytical practices, and the wastewater’s composition on WBE performance. Conclusions: This review calls for further investigation into economical evaluation methods of these factors to enhance WBE data normalization and interpretation, utilizing existing wastewater treatment plant data used for treatment control, which could be a cost-effective approach over more expensive population biomarkers. This approach, aside from SARS-CoV-2, holds potential for application to a broader number and types of diseases, as well as population consumption habits.