Pharmaceuticals of emerging concern (acetaminophen (ACM), trimethoprim (TMP), oxytetracycline (OTC), and sulfamethoxazole (SMX)) were detected in water samples from aquaculture environments and nonaquaculture sites in four regions located on the northern coast of Central Java. ACM was the most prevalent pharmaceutical, with a mean concentration ranging from not detected (n.d.) to 5.5 ± 1.9 ngL−1 (Brebes). Among the target antibiotics (TMP, OTC, SMX), OTC was the most ubiquitous, with a mean concentration varying from n.d. to 8.0 ± 3.3 ngL−1. Correlation analysis demonstrated that there was a significant correlation between TMP and SMX concentrations. Based on ecological risk assessment evaluation, the use of OTC requires serious consideration, as it presented high health risks to algae, while ACM, TMP, and SMX posed an insignificant to moderate risk to algae, invertebrates, and fish. The findings obtained from this study highlight OTC as an emerging contaminant of prominent concern. More attention needs to be given to managing and planning for the sustainable management of shrimp farms, particularly in the northern part of Central Java.