Abstract The present study aims to investigate the variability of catches by trawling fleet vessels licensed to operate under the ‘diverse fish’ license in relation to the depth gradient and the hydrological cycle of the Amazon River. For this purpose, vessels operating in this category were accompanied by on-board observers on the inner Amazon shelf, during January, April and July 2013 and in April, May, August and September 2014. A total of 115,505 kg of fish was harvested, distributed among 22 species. The flood period was the most representative, with a total of 43,122 kg, followed by the ebb period (28,749 kg), the rainy period (23,171 kg) and the dry period (20,424 kg). Kingfish (Macrodon ancylodon) was the most abundant fish in all seasons (79.7%). Significant differences were observed in fish composition in relation to the depth gradient and hydrodynamics of the Amazon River, with higher richness and diversity (Margalef index) during flood periods and at greater depths throughout the study period. We also observed a significant interaction between river flow and depth category, with more diversified fish fauna attributed to ebbs and floods in shallow and deep waters at the mouth of the Amazon River. Considering that the license for ‘diverse fish’ was established as an alternative to fishing for marine shrimp in closed season, the need for effective monitoring of this fishing system is reiterated for an efficient assessment of the impacts in the fish community structure.