A 200-kHz split-beam echosounder (BioSonics, DT6000) with a 6° circular-beam transducer was applied in a mangrove channel in Northern Brazil to study the migratory patterns of intertidal fish. Acoustic sampling was conducted horizontally across the channel perpendicular to the tidal current during two lunar cycles in the dry season 2000 and the wet season 2001. The complex acoustic environment of the mangrove channel was characterized by small target sizes (juvenile fish), multiple targets (aggregated fish), high reverberation and background noise levels due to sediment loads, plankton and mangrove litter transport. Dry seasons provided less noisy acoustic conditions resulting in clearer echo data than wet seasons. Neap tide data were less complex than spring tide data. During a tidal cycle, low water provided the clearest acoustic conditions. Mangrove leaves generated fish-like echoes. Analysis of two dry season wax moon cycles revealed fish flux maxima at low water, flood start and high water in the daytime and the night cycle. Night fish fluxes were significantly higher than at daylight. Throughout the tidal cycles, 60% of the fish traveled with the tide and 40% against, suggesting active foraging against the tide to be a major component of fish movements. Resident mangrove fish entered the intertidal creeks at early flood tide, leaving at late ebb tide at fairly shallow-water depths. Estuarine fish required a minimum water depth (about 2 m) for tidal migration. Since time delays during spring tides between immigration of resident and estuarine fish were reduced, foraging time and habitat accessibility would be enhanced and fish catches and fishes’ feeding success would be greater.