Muling River, situated amidst cultivated lands in Heilongjiang Province, northeastern China, has long been subjected to sand-digging activities, resulting in severe damage to its riverbed. However, little research has been conducted on the impact of this disturbance on the status of fish community structure and trophic guilds in this river. In this study, environmental factors, fish community structure, and their trophic guilds biomass distribution patterns from Muling River basin were investigated along season (spring, summer, and autumn) and section (upper, middle, and lower stream) gradient both of 2015 and 2017. During the six sampling times periods, 46 species of five orders and 12 families of fish classified into seven trophic guilds. Fish species number and biomass were highest at the first five sampling sites. The insectivores (16.26%), phytoplanktivores (10.09%), benthivores (40.17%), and omnivores (11.86%) were the dominant trophic guilds. We find that fish trophic guilds biomass in upper-stream was significantly different from other section (p.adjusted < 0.01), while SD, WD, PH, TP and COD_Mn were highest in the upper section. Variation partitioning revealed that fish trophic guilds biomass was influenced more by environmental factors (61.2%), followed by section (0.7%) and season (0.1%). Partial RDA ordination showed that fish trophic guilds were positively correlated with water depth and transparency, while negative with turbidity. This study underscores the importance of considering trophic guilds of freshwater fishes to inform management strategies in regions experiencing significant environmental change.