Phthalate Esters (PAEs), detected in high concentrations generally in treated wastewater discharged from wastewater treatment plants (WWTPs), are important pollutants that restrict the reuse of wastewater. Investigating the fate of these endocrine-disrupting chemicals in WWTPs is crucial in order to protect both receiving environments and ecosystems. For this purpose, di(2-ethylhexyl) phthalate (DEHP), di-n-octyl phthalate (DNOP) and benzyl butyl phthalate (BBP) in the group of PAEs were monitored in simultaneously both in wastewater and sludge lines of selected two nature-based WWTPs and one advanced biological WWTP. Although it was frequently stated that phthalates were significantly removed in WWTPs in many studies found in literature, negative removal efficiencies of selected phthalates in investigated WWTPs during the sampling period were observed generally in this study. One of the reasons for this concentration increase could be releasing of phthalates from microplastics in wastewater during the treatment process or the desorption of PAEs from treatment sludge. DNOP was the compound with the highest concentration increase at almost each treatment unit of the three WWTPs. On the other hand, total PAEs load was 1997 g d−1 in advanced biological WWTP and adsorption onto sludge of PAEs were determined as 90%. The side-stream total load returned from the decanter supernatant was 0.02% of the total PAEs load coming to advanced biological WWTP from the sewer system. As a result of detailed statistical analysis, the correlation between raw wastewater and primary clarifier (PC) effluent was determined as an increasing linear relation for DEHP and DNOP. On the other hand, moderate and strong correlations were observed both between septic tank and constructed wetland (CW) processes with raw wastewater. In the waste stabilization pond (WSP), while a significant correlation was not found between the sludge line data, homogeneous variance, strong and moderate correlations were obtained in the wastewater line data. However, while mean differences for all investigated PAEs were not significant (p > 0.05) in the wastewater line, mean differences of DEHP (p < 0.05) were significant in the sludge line according to ANOVA analysis.