A characteristic feature of the eastern Bering Sea (EBS) is a subsurface layer linked to seasonal sea ice (SSI) and defined by bottom temperatures less than 2 °C, which is termed the cold pool. Cold pool variability is directly tied to regional zooplankton and fish dynamics. Multifrequency (200 and 460 kHz) acoustic backscatter data were collected remotely using upward looking echosounders along the EBS shelf from 2008 and 2018 and used as a proxy of biological abundance. Acoustic data were coupled with bottom temperature and regional SSI data from the cold (2006–2013) and warm (2014–2018) regimes to assess the relationship between biological scattering communities and cold pool variation. Acoustic backscatter was 2 orders of magnitude greater during the cold regime than during the warm regime, with multifrequency analysis indicating a shift in the warm regime frequency-dependent scattering communities. Cold pool proxy SSI was a stronger predictor for biological scattering than bottom temperature in the cold regime, while warm regime bottom temperature and SSI were equal in predictive power and resulted in improved predictive model performance. Results suggest coupled cold pool and frequency-dependent scattering dynamics are a potential regime shift indicator and may be useful for management practices in surrounding Arctic ecosystems.