Estuaries in South Africa are very important for biodiversity conservation and serve as focal points for leisure and tourism activities. The organophosphate flame retardants (OPFRs) levels in these aquatic systems haven't been documented in any studies as of yet. Due to the negative effects of persistent organic pollutants in South African estuaries, we examined the occurrence of eight OPFRs in sediments of two estuaries by studying their spatiotemporal distribution, season variation, and ecological risks. The Sundays Estuary (SDE), a semi-urbanized agricultural surrounding system, recorded an ∑8OPFR concentration in sediments that ranged from 0.71 to 22.5 ng/g dw, whereas Swartkops Estuary, a largely urbanized system, recorded a concentration that ranged from 0.61 to 119 ng/g dw. Alkyl-OPFRs were the prevalent homologue in both estuaries compared to the chlorinated and aryl groups. While TBP, TCPP, and TCrP were the most abundant compounds among the homologue groups. There was no distinct seasonal trend of ∑8OPFR concentration in either estuary, with summer and autumn seasons recording the highest concentrations in SDE and SWE, respectively. Ecological risks in the majority of the study sites for the detected compounds were at low (RQ < 0.1) and medium levels (0.1 ≤ RQ < 1) for certain species of fish, Daphnia magna and algae. However, the cumulative RQs for all the compounds had ∑RQs ≥1 for most sites in both estuaries, indicating that these organisms, if present in both estuaries, may be exposed to potential ecological concerns due to accumulated OPFR chemicals. The scope of future studies should be broadened to include research areas that are not only focus on the bioaccumulation patterns of these compounds but also find sustainable ways to reduce them from these estuarine environments.