Trophic dynamics of integrated rice and fish farming (IRF) systems were studied in irrigated rice plots stocked with common carp in Madagascar. Fish feeding behavior was assessed by analyzing stable carbon and nitrogen isotopes of fish and natural feed sources. Stable isotope signatures of 45-day-old carp fry introduced into rice plots (d13C = -18.8‰ ± 0.5‰, d15N = 9.3‰ ± 0.6‰) revealed that they had been fed chicken egg yolk and corn meal, in accordance with local practices. However, after a 100-day growing period in experimental rice plots, 13C and 15N depletion was observed for 145-day-old carp, indicating a change in feeding sources. Under extensive conditions, common carp that fed on rice roots, sediments and suspended particulate organic matter (i.e. plant debris and detritus) had a larger trophic niche (3‰2) than 45-day-old carp (1.2‰2). Overall, common carp feeding behavior and the trophic food web in the IRF system suggest that increasing natural productivity through organic fertilization will enhance ecological intensification of both rice and fish production.