The management of emerging pollutants (EPs) in wastewater treatment is a challenging task that demands a nuanced understanding of pollutant characteristics, analytical methodologies, and environmental factors. This chapter delves into the limitations encountered in the detection and removal of EPs with a special emphasis on types and analysis of pollutants, instrumentation constraints, and diverse environmental variables. Firstly, it scrutinizes the limitations arising due to the diversity of pollutants, encompassing their varied chemical compositions and behavioral characteristics. Additionally, it examines the inadequacies of existing analytical techniques in the effective detection and quantification. Apart from these challenges, the influence of environmental factors—including temperature, pH, total dissolved solids (TDS)Total Dissolved Solids (TDS), biological oxygen demand (BOD), density, viscosity, atomic weight, and atomic mass—on pollutant detection and removal processes, highlighting their intricate interplay with treatment efficacy has been incorporated. Drawing insights from these limitations, the subsequent section delineates recommendations and suggestions to overcome these hurdles. The current proposal encompasses the innovative analytical methodologies, the use of advanced instrumentation, and improved understanding of environmental dynamics. Finally, the chapter concludes by emphasizing the imperative of continuous research and technological innovation in surmounting these limitations and advancing sustainable solutions for pollutant management in wastewater treatment systems.