The present experiment was conducted to assess the effects of decomposing rice straw on algal flora as well as physical, chemical, and biological-parameters of 9 earthen fish ponds of 2100m3 for each with one-meter average depth. It was conducted for 6 months using three treatments. Each pond was stocked with 6000 fish fries of Nile tilapia (Oreochromis niloticus). Results showed that water quality decreased with increased loading rates of rice straw. Most of water quality parameters including EC, TDS, total alkalinity, total phosphorus, NO3, NO2, chlorophyll a, and pH were significantly lower in rice straw treatments than control. Total ammonia, Secchi disc visibility and orthophosphate were significantly higher with increase rice straw loading than  control. Cyanophyceae constituted the dominant algal group at the initial phase at all examined ponds. This dominance remained stable in control ponds by the end of experiment. In contrast, in the final stage of the experiment Chlorophyceae and Bacillariophyceae dominate in T2 and T3 treatments compared with control. The results of this work illustrated that the decrease of algal count was related to action of allelochemicals discharged from rice straw aqueous extract leading to suppress growth of some algal species. Hence, this technique is a way to reduce the cost and reduce the use of herbicides, by providing natural compounds that can be obtained from agricultural waste.