Micro-estuarine ecosystems have a surface area <1 km2 and are abundant in Mediterranean regions. As a result of their small size, these systems are particularly vulnerable to the effects of chemical pollution. Due to the fluctuating flow conditions of base flow dominated by treated wastewater effluents and flood events transporting rural and urban non-point-source pollution, micro-estuaries are under a dynamic risk regime, consequently struggling to provide ecological services. This 2 year study explored the occurrence and risks of pharmaceutical contamination in the Alexander micro-estuary in Israel. Pharmaceuticals were detected in all samples (n = 280) at as high as 18 μg L-1 in flood events and 14 μg L-1 in base flow. The pharmaceutical mixture composition was affected by flow conditions with carbamazepine dominating the base flow and caffeine dominating flood events. The median annual risk quotients for fish, crustaceans, and algae were 19.6, 5.2, and 4.5, respectively, indicating that pharmaceuticals pose a high risk to the ecosystem. Ibuprofen, carbamazepine, and caffeine contributed most to the risk quotients. The current work highlights that micro-estuary ecosystems, like the Alexander estuary, are continuously exposed to pharmaceuticals and most likely to other pollutants, placing these ecologically important systems under an elevated risk in comparison to the more frequently studied large estuarine systems.