Macrozooplankton plays a key role in pelagic ecosystems as a link between lower trophic levels and fish. However, although its ecological role is usually considered in polar ecosystems, it is rarely considered in temperate ones. To obtain comprehensive information on the macrozooplankton distribution in the Bay of Biscay we adapted a bi-frequency acoustic method developed for the Humboldt Current system. This method can be used to extract continuous and simultaneous high-resolution information on the spatiotemporal patterns of biomass distributions of macrozooplankton and pelagic fish throughout the diel cycle. The 2 distributions were mapped using geostatistical techniques. We applied kriging with external drifts, which accounts for both diel and across-shore changes in macrozooplankton biomass. We then used a cross-variogram to determine the scale-dependent relationships between macrozooplankton and fish. The results show how macrozooplankton and fish are distributed according to the different ecological domains (coast, shelf, shelf-break and offshore) along the Spanish and French coasts. Specific macrozooplankton hotspots were observed, but macrozooplankton was generally more abundant offshore than inshore, whereas fish showed the opposite trend. This pattern was confirmed by the aggregation sizes, which increased towards oceanic waters for macrozooplankton and decreased for fish. Finally, the correlation between fish and macrozooplankton was positive on a small scale (<30 nautical miles) and negative on a large scale (>30 nautical miles).