The study was performed in earthen ponds situated in North- Nile Delta, Egypt and adopted two fish farming systems. The first system was the feed fish farm that depended on pelleted diet (25% crude protein) as feed input, while the other system was the fertilizer fish farm which utilized both organic fertilizer and crushed macaroni as supplementary feed. Each system had four replicate ponds (8400 m² each). The experiment duration was one year, including four months of over-wintering. 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. Samples were collected to determine water quality, plankton abundance and fish growth performance. The results showed that the fertilizer fish farm had significantly high levels of pH, dissolved oxygen and total nitrogen content (TAN, NH₃, NH₄, NO₂ and NO₃) (P<0.05). Significant increase (P<0.05) in phytoplankton and zooplankton abundance was observed in the fertilizer fish farm compared to the feed fish farm. Within different species, catfish had the highest daily weight gain followed by tilapia and mullet, respectively. Within the two compared systems, farmed fish in the feed farm had higher average daily weight gain and specific growth rate. The feed fish farm had significantly (P<0.05) higher production and higher total income, while the fertilizer fish farm had higher net income and lower total production costs.