Anthropogenic underwater noise has emerged as a growing stressor in aquatic ecosystems, with negative impact on fish physiology, sensory adaptation, behavior, and survival. This chapter reviews current knowledge on the fish species most commonly used to investigate the effects of noise pollution, highlighting the advantages and limitations of freshwater versus marine models, while also proposing guidelines for species selection. While zebrafish has been widely used as a freshwater model, the marine medaka is presented as a promising model species for ecotoxicology and noise pollution research. Furthermore, studies indicate that molecular and physiological alterations, such as transcriptomic changes and endocrine disruption, can occur even in the absence of evident behavioral changes, highlighting the need for integrative approaches. By integrating behavioral, physiological, and molecular approaches with model organisms that allow high-throughput screening of ecotoxicology effects, this chapter outlines strategies for improving noise pollution research.