Abstract: Background and Objective: Aquaponic is a type of recirculating aquaculture system where plant and fish provide suitable media for the development of each. The lipid classes, fatty acids profile and ovary structure of Nile tilapia Oreochromis niloticus reared in this type of system aquaponic parents (AP) and also their first generation aquaponic progeny (AG) allowed to develop in this system till ripening and were evaluated and compared with control parent (CP) and control progeny (CG) reared in normal aquaria. Methodology: Oreochromis niloticus larvae were introduced to aquaponic (AP) and control (CP) rearing tanks (40 fish for each). When females in aquaponic and control groups (AP and CP) about to spawn, they were removed with spermiating males of their groups to continue fertilization process. After hatching (15 day old fries) were transported to their corresponding tanks. When fishes reach maturity, females from each aquaponic group as well as from the control parent and progeny were sacrificed then ovaries were used for determination of lipid content, lipid fatty acids profile as well as ratio of deformed oocytes. Data were analyzed using one-way analysis of variance (ANOVA) at significance of (p<0.05). Results: This study showed insignificant differences in lipid class, fatty acid profile among AP and CP groups and an alteration in ovaries lipid content and class-composition of AG group relative to CG, recording significantly (p<0.05) higher triglycerides (TG) level, lowered total lipid (TL), cholesterol (COL) and phospholipid (PL) levels. Fatty acids profile alterations occurred in ovary of AG fish relative to CG fish. Saturated fatty acids significantly decrease (p<0.05) and MUFA increased (p<0.05). Levels of Eicosapentaenoic acid (EPA), Docosahexaenoic acid (DHA) and Arachidonic acid (ARA) fatty acids showed insignificant variation in ovaries of aquaponic groups. Histological examination of ovaries indicated significant increase in percentage of deformed oocytes in AG group. Deformation was restricted to mature and maturing oocytes. Conclusion: Aquaponic rearing conditions affect Nile tilapia progeny reared to maturity in this type of system, causing significant decrease in total lipid content, altered fatty acid classes and fatty acids profile and increase percentage of deformed oocytes.