The Adriatic Sea is vulnerable to pollution due to its low bathymetry, intense industrial activity, and tourism. In this context, a good depuration plant activity could play a key role for the maintenance of a good environmental quality. In the framework of the AdSWiM project, “Managed use of treated urban wastewater for the quality of the Adriatic Sea”, a study on dissolved potentially toxic element (PTE) levels was carried out to assess the impact of treated urban wastewaters on the quality of the bathing waters in the Adriatic Sea during the 2019 and 2020 summer period. In the present study, three areas along the Italian–Croatian coastline (Gulf of Trieste, Zadar, and Split) were identified for the monitoring of five depuration plant (DP) outflows. Water samples were collected after the treatment inside the DPs, and coastal seawater was sampled in the proximity of the discharging pipelines. Dissolved Hg, Cd, and As levels were determined with an atomic fluorescence spectrometer. Results did not show statistically significant differences between treated wastewater and seawater samples (Hg 10 ± 6 and 10 ± 4, Cd 14 ± 6 and 21 ± 8, As 610 ± 176 and 687 ± 140 ng L−1, respectively), while the geographical area and the seasonality affected the PTE concentration. Furthermore, the levels detected were lower than the European and national limits, indicating a good environmental status of the northern Adriatic Sea waters. The determination of further parameters (nutrients, microbiological indicators) must be investigated to identify possible synergistic effects. However, our results demonstrate the efficiency of DPs investigated, underlining the importance of the wastewater treatment for the protection of the Adriatic Sea.