Phthalate compounds in sediments and fishes were investigated in 17 Taiwan’s rivers to determine the relationships between phthalate levels in sediment and aquatic factors, and biota-sediment accumulation factor (BSAF) for phthalates. Mean concentrations (range) of di(2-ethylhexyl) phthalate (DEHP), butyl benzyl phthalate (BBzP) and di-n-butyl phthalate (DBP) in sediment at low-flow season were 4.1 (<0.05–46.5), 0.22 (<0.05–3.1) and 0.14 (<0.05–1.3) mg kg−1 dw; those at high-flow season were 1.2 (<0.05–13.1), 0.13 (<0.05–0.27) and 0.09 (<0.05–0.22) mg kg−1 dw, respectively. Trace levels of dimethyl phthalate (DMP), diethyl phthalate (DEP) and di-n-octyl phthalate (DOP) in sediment were found in both seasons. Concentrations of DEHP in sediments were significantly affected by temperature, suspended solids, ammonia–nitrogen, and chemical oxygen demand. The highest concentration of DEHP in fish samples were found in Liza subviridis (253.9 mg kg−1 dw) and Oreochromis miloticus niloticus (129.5 mg kg−1 dw). BSAF of DEHP in L. subviridis (13.8–40.9) and O. miloticus niloticus (2.4–28.5) were higher than those in other fish species, indicating that the living habits of fish and physical–chemical properties of phthalates, like log Kow, may influence the bioavailability of phthalates in fish. Our data suggested that DEHP level in river sediments were influenced by water quality parameters due to their effects on the biodegradation processes, and that the DEHP level in fish was affected by fish habitat and physiochemical properties of polluted contaminants.