Major carps, native freshwater fish in South Asian nations, are economically valuable fish species with high market demand. Coastal rural people can cultivate them in their own seasonal, largely underutilized, small homestead ponds with low input and understanding. However, the major problems with fish production in this region are the lack of quality carp seed and appropriate culture techniques. Therefore, this research was carried out on growth performance, survival rate, yield, feed conversion ratio (FCR), and profit of carp polyculture systems stocking with hatchery-produced and wild sourced fish seed in homestead ponds located in a coastal area along the Bay of Bengal. Three different treatments (T1–T3), each treatment with three replications, were designed for culturing carps, Gibelion catla, Labeo rohita, Labeo calbasu, and Cirrhinus mrigala using two local hatcheries seeds (T1 and T2), and wild seeds from the Halda River (T3). For all treatments, the stocked fish were maintained in the same size, weight, density, and ratio. Water quality parameters were measured at intervals of seven days, and the mean values were found to be within an acceptable range for fish farming and, in most cases, did not differ significantly from each other. The specific growth rate (SGR) was found higher in T3 for G. catla (1.16 ± 0.012%/day), L. rohita (1.19 ± 0.035%/day), and C. mrigala (1.06 ± 0.03%/day) and significantly differed (p < 0.05) among the treatments. Additionally, there were significant differences between the treatments in terms of ultimate weight, weight gain, survival rate, fish production, and return on investment (ROI) (p < 0.05). The lower FCR in T3 (2.65 ± 0.10) than in T1 (3.32 ± 0.31) and T2 (3.21 ± 0.33) indicated that stocking wild seed had higher profitability potentials. High genetic variety in the population of naturally occurring, free-living fish, resistance to disease, a high rate of survival, and the hardiness of wild seed are all factors that might contribute to the better performance of wild seed stock. However, the total yield and total return from the T3 treatment also emphasized that carp farming using wild seed is not viable because of the variable amount, high seed cost, low transportation facilities, and very small natural seed-stock supplies from the river. Inbreeding and reduced genetic variety in the hatchery stock could result in the production of poor-quality seed, which had an impact on the production performance in culture treatments stocked with hatchery seed.