The study was conducted in two fish farming systems in earthen ponds located in North- Nile Delta, Egypt. The first system was the feed fish farm that depended on pelleted diet (25% crude protein) as feed input, while the second system was the fertilizer fish farm which used both organic fertilizer and crushed macaroni as supplementary feed. Each system was replicated in four ponds (8400m² each). The experimental period lasted from July 2014 to June 2015, including four months overwintering. Nile tilapia (Oreochromis niloticus), mullet (Mugil cephalus) and catfish (Clarias gariepinus) were cultured in each pond at initial weight of 2, 30 and 5 grams, respectively. Water, sediment and fish samples were collected to detect the heavy metals concentration. The results showed that heavy metals concentration in water, sediment and three organs of fish species were significantly (P<0.05) different between the feed and fertilizer fish farms. The pond management affected the content of heavy metals in water, sediments and fish. Accumulation of iron in water, sediment and three organs of fish were higher than other elements. Accumulation of cadmium and lead in water, sediment and three organs of fish were less than other elements. Accumulation of heavy metals in liver and gills were higher than that of muscles in all fish species. Metals concentrations in the edible part of farmed fish were within the permissible level for human consumption proposed by various international standard organizations.