Efficient photocatalysts for the simultaneous removal of organic dyes and antibiotics are crucial for sustainable environmental management. In this study, we designed and synthesized a C3N5/BiO2-x S-type heterojunction photocatalyst with structural defects using a hydrothermal method, aimed at degrading both Rhodamine B (RhB) and tetracycline (TC). The degradation kinetic constants for RhB and TC were 0.0809 min−1 and 0.0535 min−1, respectively, showing improvements of 9.52 and 25.48 times over pure C3N5, and 2.90 and 1.49 times over BiO2-x. This enhanced performance is attributed to the unique electron transfer mechanism of the S-scheme heterojunction and the structural defects that facilitate efficient separation of electron-hole (e−-h+) pairs. Free radical trapping experiments indicated that the main reactive oxygen species (ROS) involved are ·O2− and h+. Additionally, electrochemical impedance spectroscopy (EIS) and transient photocurrent response (TPR) measurements confirmed improved separation and transfer of photogenerated e−-h+ pairs in the C3N5/BiO2-x heterojunction. The higher density of structural defects in C3N5/BiO2-x compared to individual BiO2-x counterparts enhances its ability to activate and photo-oxidize TC and degrade RhB. Consequently, C3N5/BiO2-x demonstrates significant potential as a photocatalyst for improving water quality.