The River Ganga produces a substantial amount of its fish from small native species, defined here as those with a maximum length of 25 cm. The FiSAT program was utilized to estimate stock assessments of four important small indigenous species from the River Ganga: Johnius coitor, Cabdio morar, Salmostoma bacaila, and Gudusia chapra. Fish samples were collected monthly for a year (April 2020–May 2021) from four predetermined sampling sites along the River Ganga (Farakka, Berhampore, Balagarh, and Tribeni) in West Bengal, India. The estimated exploitation rate for Johnius coitor, Salmostoma bacaila, and Gudusia chapra was relatively lower than the optimum level of 0.5 and considerably lower than E_max values, indicating that their stocks are experiencing low fishing pressure in the region. The FiSAT results indicated that the species Cabdio morar was found to be heavily exploited. The total mortality (Z), natural mortality (M), and fishing mortality (F) rates for all four of the SIF species were examined, and they were contrasted with data from previous studies. On the lower stretch of the River Ganga, all of the fish stocks are optimally exploited (E_opt), except for the species Cabdio morar. The population dynamics of all of the species have been described for the first time on the lower stretch of the River Ganga. According to the findings, all of the fish stocks throughout the lower stretch of River Ganga are optimally exploited (E_opt), except for Cabdio morar. The study also emphasizes the importance of increasing sustainable fishing efforts, focusing on SIFs throughout the lower stretch of the River Ganga in order to safeguard the livelihood and nutritional status of fishermen.